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Conserved domains on  [gi|1907067540|ref|XP_036018346|]
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KH domain-containing, RNA-binding, signal transduction-associated protein 2 isoform X1 [Mus musculus]

Protein Classification

KH domain-containing protein( domain architecture ID 11242095)

K homology (KH) domain-containing protein may bind single-stranded RNA or DNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
KH-I super family cl00098
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 54-171 2.46e-73

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.


The actual alignment was detected with superfamily member cd22469:

Pssm-ID: 469614 [Multi-domain]  Cd Length: 118  Bit Score: 220.38  E-value: 2.46e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907067540  54 SNKNIKLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKTKEEELRKSGEAKYAHLSDELHV 133
Cdd:cd22469     1 SNKNIKLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKAKEEELRKSGEAKYAHLSDELHV 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1907067540 134 LIEVFAPPGEAYSRMSHALEEIKKFLVPDYNDEIRQEQ 171
Cdd:cd22469    81 LIEVFAPPGEAYSRMSHALEEIKKFLVPDYNDEIRQEQ 118
Qua1 pfam16274
Qua1 domain; This domain, approximately 40 residues in length, is mainly found in KH-domain ...
 5-57 5.83e-24

Qua1 domain; This domain, approximately 40 residues in length, is mainly found in KH-domain containing, RNA-binding, signal transduction-associated protein 1 from yeast to human. It forms a homodimer composed of a perpendicular interaction of two helical hairpins, and the Qua1 domain is sufficient for homodimerization which is required for the regulation of alternative splicing.


:

Pssm-ID: 465079  Cd Length: 52  Bit Score: 91.33  E-value: 5.83e-24
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907067540   5 KYLPELMAEKDSLDPSFVHASRLLAEEIEKFQGSDGKKEDEEkKYLDVISNKN 57
Cdd:pfam16274   1 KYLPELMAEKDSLDPSFTHAMQLLSAEIEKIQKGESKKDDEE-KYLDLFSNKN 52
 
Name Accession Description Interval E-value
KH-I_KHDRBS2 cd22469
type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal ...
 54-171 2.46e-73

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 2 (KHDRBS2) and similar proteins; KHDRBS2, also called Sam68-like mammalian protein 1, or SLM-1, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds both poly(A) and poly(U) homopolymers. KHDRBS2 may function as an adapter protein for Src kinases during mitosis.


Pssm-ID: 411897 [Multi-domain]  Cd Length: 118  Bit Score: 220.38  E-value: 2.46e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907067540  54 SNKNIKLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKTKEEELRKSGEAKYAHLSDELHV 133
Cdd:cd22469     1 SNKNIKLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKAKEEELRKSGEAKYAHLSDELHV 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1907067540 134 LIEVFAPPGEAYSRMSHALEEIKKFLVPDYNDEIRQEQ 171
Cdd:cd22469    81 LIEVFAPPGEAYSRMSHALEEIKKFLVPDYNDEIRQEQ 118
Qua1 pfam16274
Qua1 domain; This domain, approximately 40 residues in length, is mainly found in KH-domain ...
 5-57 5.83e-24

Qua1 domain; This domain, approximately 40 residues in length, is mainly found in KH-domain containing, RNA-binding, signal transduction-associated protein 1 from yeast to human. It forms a homodimer composed of a perpendicular interaction of two helical hairpins, and the Qua1 domain is sufficient for homodimerization which is required for the regulation of alternative splicing.


Pssm-ID: 465079  Cd Length: 52  Bit Score: 91.33  E-value: 5.83e-24
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907067540   5 KYLPELMAEKDSLDPSFVHASRLLAEEIEKFQGSDGKKEDEEkKYLDVISNKN 57
Cdd:pfam16274   1 KYLPELMAEKDSLDPSFTHAMQLLSAEIEKIQKGESKKDDEE-KYLDLFSNKN 52
MSL5 COG5176
Splicing factor (branch point binding protein) [RNA processing and modification];
59-181 7.62e-18

Splicing factor (branch point binding protein) [RNA processing and modification];


Pssm-ID: 227503 [Multi-domain]  Cd Length: 269  Bit Score: 80.78  E-value: 7.62e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907067540  59 KLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMrdktKEEELRKSGEAKYAHLSDELHVLIEVF 138
Cdd:COG5176   147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSV----KEGKISSDTPESLKNAEAVLHCLIEAD 222

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1907067540 139 APPGEAYSRMSHALEEIKKFLVPDYNDEIRQEQLRELSYLNGS 181
Cdd:COG5176   223 SEDKICRLIKSQLNAIREARRNPEGQNDLKRFQLRWLAHLNGT 265
KH smart00322
K homology RNA-binding domain;
59-106 7.13e-06

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 43.05  E-value: 7.13e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1907067540   59 KLSERVLIPVkqypkfNFVGKLLGPRGNSLKRLQEETGAKMSILGKGS 106
Cdd:smart00322   2 PVTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS 43
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 61-106 1.14e-05

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.


Pssm-ID: 459630 [Multi-domain]  Cd Length: 65  Bit Score: 42.27  E-value: 1.14e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1907067540  61 SERVLIPVKQypkfnfVGKLLGPRGNSLKRLQEETGAKMSILGKGS 106
Cdd:pfam00013   1 TVEILVPSSL------VGLIIGKGGSNIKEIREETGAKIQIPPSES 40
 
Name Accession Description Interval E-value
KH-I_KHDRBS2 cd22469
type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal ...
 54-171 2.46e-73

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 2 (KHDRBS2) and similar proteins; KHDRBS2, also called Sam68-like mammalian protein 1, or SLM-1, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds both poly(A) and poly(U) homopolymers. KHDRBS2 may function as an adapter protein for Src kinases during mitosis.


Pssm-ID: 411897 [Multi-domain]  Cd Length: 118  Bit Score: 220.38  E-value: 2.46e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907067540  54 SNKNIKLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKTKEEELRKSGEAKYAHLSDELHV 133
Cdd:cd22469     1 SNKNIKLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKAKEEELRKSGEAKYAHLSDELHV 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1907067540 134 LIEVFAPPGEAYSRMSHALEEIKKFLVPDYNDEIRQEQ 171
Cdd:cd22469    81 LIEVFAPPGEAYSRMSHALEEIKKFLVPDYNDEIRQEQ 118
KH-I_KHDRBS cd22384
type I K homology (KH) RNA-binding domain found in the KH domain-containing, RNA-binding, ...
 56-157 6.85e-66

type I K homology (KH) RNA-binding domain found in the KH domain-containing, RNA-binding, signal transduction-associated protein (KHDRBS) family; The KHDRBS family includes three members, KHDRBS1-3. KHDRBS1, also called GAP-associated tyrosine phosphoprotein p62, or Src-associated in mitosis 68 kDa protein, or Sam68, or p21 Ras GTPase-activating protein-associated p62, or p68, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS1 acts as a putative regulator of mRNA stability and/or translation rates and mediates mRNA nuclear export. It is recruited and tyrosine phosphorylated by several receptor systems, for example the T-cell, leptin and insulin receptors. KHDRBS2, also called Sam68-like mammalian protein 1, or SLM-1, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds both poly(A) and poly(U) homopolymers. KHDRBS2 may function as an adapter protein for Src kinases during mitosis. KHDRBS3, also called RNA-binding protein T-Star, or Sam68-like mammalian protein 2, or SLM-2, or Sam68-like phosphotyrosine protein, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds optimally to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS3 may play a role as a negative regulator of cell growth.


Pssm-ID: 411812 [Multi-domain]  Cd Length: 102  Bit Score: 200.59  E-value: 6.85e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907067540  56 KNIKLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKTKEEELRKSGEAKYAHLSDELHVLI 135
Cdd:cd22384     1 KPIKLSEKVLIPVKEFPKFNFVGKLLGPRGNTLKRLQEETGTKMSILGKGSMRDKAKEEELRKSGDPKYAHLNEDLHVLI 80

                          90       100
                  ....*....|....*....|..
gi 1907067540 136 EVFAPPGEAYSRMSHALEEIKK 157
Cdd:cd22384    81 EAFAPPAEAYARLAHALAELRK 102
KH-I_KHDRBS1 cd22468
type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal ...
 56-161 2.05e-60

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 1 (KHDRBS1) and similar proteins; KHDRBS1, also called GAP-associated tyrosine phosphoprotein p62, or Src-associated in mitosis 68 kDa protein, or Sam68, or p21 Ras GTPase-activating protein-associated p62, or p68, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS1 acts as a putative regulator of mRNA stability and/or translation rates and mediates mRNA nuclear export. It is recruited and tyrosine phosphorylated by several receptor systems, for example the T-cell, leptin and insulin receptors.


Pssm-ID: 411896 [Multi-domain]  Cd Length: 106  Bit Score: 186.76  E-value: 2.05e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907067540  56 KNIKLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKTKEEELRKSGEAKYAHLSDELHVLI 135
Cdd:cd22468     1 KNMKLKERILIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKGSMRDKAKEEELRKGGDPKYAHLNMDLHVFI 80

                          90       100
                  ....*....|....*....|....*.
gi 1907067540 136 EVFAPPGEAYSRMSHALEEIKKFLVP 161
Cdd:cd22468    81 EVFGPPCEAYARMAHAMEEVKKFLVP 106
KH-I_KHDRBS3 cd22470
type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal ...
 52-164 2.16e-59

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 3 (KHDRBS3) and similar proteins; KHDRBS3, also called RNA-binding protein T-Star, or Sam68-like mammalian protein 2, or SLM-2, or Sam68-like phosphotyrosine protein, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds optimally to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS3 may play a role as a negative regulator of cell growth.


Pssm-ID: 411898 [Multi-domain]  Cd Length: 113  Bit Score: 184.48  E-value: 2.16e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907067540  52 VISNKNIKLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKTKEEELRKSGEAKYAHLSDEL 131
Cdd:cd22470     1 VVINKNMKLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGEAKYFHLNDDL 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1907067540 132 HVLIEVFAPPGEAYSRMSHALEEIKKFLVPDYN 164
Cdd:cd22470    81 HVLIEVFAPPAEAYARMGHALEEIKKFLIPDYN 113
KH-I_Hqk_like cd22383
type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) family; The Hqk ...
 59-161 7.35e-42

type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) family; The Hqk family includes Hqk and protein held out wings (how) found in Drosophila. Hqk, also called HqkI, is an RNA-binding protein that plays a central role in myelinization. It binds to the 5'-NACUAAY-N(1,20)-UAAY-3' RNA core sequence and regulates target mRNA stability. It acts by regulating pre-mRNA splicing, mRNA export and protein translation. Hqk is a regulator of oligodendrocyte differentiation and maturation in the brain that may play a role in myelin and oligodendrocyte dysfunction in schizophrenia. How, also called KH domain protein KH93F, or protein muscle-specific, or protein Struthio, or protein wings held out (who), or Quaking-related 93F (qkr93F), is an RNA-binding protein involved in the control of muscular and cardiac activity. It is required for integrin-mediated cell-adhesion in wing blade. It plays essential roles during embryogenesis, in late stages of somatic muscle development, for myotube migration and during metamorphosis for muscle reorganization.


Pssm-ID: 411811 [Multi-domain]  Cd Length: 101  Bit Score: 139.41  E-value: 7.35e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907067540  59 KLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKTKEEELRksGEAKYAHLSDELHVLIEVF 138
Cdd:cd22383     1 KLSEKVYVPVDEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMIRGKGSMRDKKKEEANR--GKPNWEHLNDDLHVLITVE 78

                          90       100
                  ....*....|....*....|...
gi 1907067540 139 APPGEAYSRMSHALEEIKKFLVP 161
Cdd:cd22383    79 DTENRAHIKLAKAVEEVKKLLIP 101
KH-I_HOW cd22466
type I K homology (KH) RNA-binding domain found in Drosophila protein held out wings (how) and ...
 58-161 1.82e-33

type I K homology (KH) RNA-binding domain found in Drosophila protein held out wings (how) and similar proteins; How, also called KH domain protein KH93F, or protein muscle-specific, or protein Struthio, or protein wings held out (who), or Quaking-related 93F (qkr93F), is an RNA-binding protein involved in the control of muscular and cardiac activity. It is required for integrin-mediated cell-adhesion in wing blade. It plays essential roles during embryogenesis, in late stages of somatic muscle development, for myotube migration and during metamorphosis for muscle reorganization.


Pssm-ID: 411894 [Multi-domain]  Cd Length: 105  Bit Score: 117.71  E-value: 1.82e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907067540  58 IKLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKTKEEELRksGEAKYAHLSDELHVLIEV 137
Cdd:cd22466     4 VTLSEKVYVPVKEHPDYNFVGRILGPRGMTAKQLEQETGCKIMVRGKGSMRDKKKEDLNR--GKPNWEHLNDELHVLITV 81

                          90       100
                  ....*....|....*....|....
gi 1907067540 138 FAPPGEAYSRMSHALEEIKKFLVP 161
Cdd:cd22466    82 EDTENRAKVKLQRAVEEVRKLLVP 105
KH-I_Hqk cd22465
type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) and similar proteins; ...
 59-161 6.05e-33

type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) and similar proteins; Hqk, also called HqkI, is an RNA-binding protein that plays a central role in myelinization. It binds to the 5'-NACUAAY-N(1,20)-UAAY-3' RNA core sequence and regulates target mRNA stability. It acts by regulating pre-mRNA splicing, mRNA export and protein translation. Hqk is a regulator of oligodendrocyte differentiation and maturation in the brain that may play a role in myelin and oligodendrocyte dysfunction in schizophrenia.


Pssm-ID: 411893 [Multi-domain]  Cd Length: 103  Bit Score: 116.58  E-value: 6.05e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907067540  59 KLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKTKEEELRksGEAKYAHLSDELHVLIEVF 138
Cdd:cd22465     1 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNR--GKPNWEHLNEDLHVLITVE 78

                          90       100
                  ....*....|....*....|...
gi 1907067540 139 APPGEAYSRMSHALEEIKKFLVP 161
Cdd:cd22465    79 DAQNRAEIKLKRAVEEVKKLLVP 101
KH-I_SPIN1_like cd22467
type I K homology (KH) RNA-binding domain found in Oryza sativa SPL11-interacting protein 1 ...
 59-161 1.65e-27

type I K homology (KH) RNA-binding domain found in Oryza sativa SPL11-interacting protein 1 (SPIN1) and similar proteins; SPIN1 is a K homology domain protein negatively regulated and ubiquitinated by the E3 ubiquitin ligase SPL11. It is involved in flowering time control in rice. SPIN1 binds DNA and RNA in vitro.


Pssm-ID: 411895  Cd Length: 101  Bit Score: 102.18  E-value: 1.65e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907067540  59 KLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKTKEEELRksGEAKYAHLSDELHVLIEVF 138
Cdd:cd22467     1 KKVLRLDVPVDKYPNFNFVGRILGPRGNSLKRVEATTGCRVFIRGRGSIKDTAKEEKLR--DKPGYEHLNEPLHVLIEAE 78

                          90       100
                  ....*....|....*....|...
gi 1907067540 139 APPGEAYSRMSHALEEIKKFLVP 161
Cdd:cd22467    79 LPANIIDARLQHAQEIIEDLLKP 101
KH-I_BBP cd02395
type I K homology (KH) RNA-binding domain found in yeast branchpoint-bridging protein (BBP) ...
 59-160 3.51e-25

type I K homology (KH) RNA-binding domain found in yeast branchpoint-bridging protein (BBP) and similar proteins; Yeast BBP, also called mud synthetic-lethal 5 protein, or splicing factor 1, or zinc finger protein BBP, is a mammalian splicing factor SF1 ortholog. It is involved in protein-protein interactions that bridge the 3' and 5' splice-site ends of the intron during the early steps of yeast pre-mRNA splicing. BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC.


Pssm-ID: 411805 [Multi-domain]  Cd Length: 92  Bit Score: 95.75  E-value: 3.51e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907067540  59 KLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKTKEEELRKSGEAkyahlSDELHVLIEvf 138
Cdd:cd02395     1 KKQRKIYIPVDEYPDYNFIGLIIGPRGNTQKRMEKESGAKIAIRGKGSVKEGKGRSDPQPDPDE-----EEDLHVLIT-- 73

                          90       100
                  ....*....|....*....|..
gi 1907067540 139 appGEAYSRMSHALEEIKKFLV 160
Cdd:cd02395    74 ---ADTEEKVDKAAKLIEKLLI 92
Qua1 pfam16274
Qua1 domain; This domain, approximately 40 residues in length, is mainly found in KH-domain ...
 5-57 5.83e-24

Qua1 domain; This domain, approximately 40 residues in length, is mainly found in KH-domain containing, RNA-binding, signal transduction-associated protein 1 from yeast to human. It forms a homodimer composed of a perpendicular interaction of two helical hairpins, and the Qua1 domain is sufficient for homodimerization which is required for the regulation of alternative splicing.


Pssm-ID: 465079  Cd Length: 52  Bit Score: 91.33  E-value: 5.83e-24
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907067540   5 KYLPELMAEKDSLDPSFVHASRLLAEEIEKFQGSDGKKEDEEkKYLDVISNKN 57
Cdd:pfam16274   1 KYLPELMAEKDSLDPSFTHAMQLLSAEIEKIQKGESKKDDEE-KYLDLFSNKN 52
MSL5 COG5176
Splicing factor (branch point binding protein) [RNA processing and modification];
59-181 7.62e-18

Splicing factor (branch point binding protein) [RNA processing and modification];


Pssm-ID: 227503 [Multi-domain]  Cd Length: 269  Bit Score: 80.78  E-value: 7.62e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907067540  59 KLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMrdktKEEELRKSGEAKYAHLSDELHVLIEVF 138
Cdd:COG5176   147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSV----KEGKISSDTPESLKNAEAVLHCLIEAD 222

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1907067540 139 APPGEAYSRMSHALEEIKKFLVPDYNDEIRQEQLRELSYLNGS 181
Cdd:COG5176   223 SEDKICRLIKSQLNAIREARRNPEGQNDLKRFQLRWLAHLNGT 265
KH-I_SF1 cd22382
type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar ...
 59-135 1.68e-17

type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar proteins; SF1, also called branch point-binding protein, or BBP, or transcription factor ZFM1, or zinc finger gene in MEN1 locus, or zinc finger protein 162, is necessary for the ATP-dependent first step of spliceosome assembly. Binds to the intron branch point sequence (BPS) 5'-UACUAAC-3' of the pre-mRNA. It may act as transcription repressor.


Pssm-ID: 411810 [Multi-domain]  Cd Length: 93  Bit Score: 75.42  E-value: 1.68e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907067540  59 KLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSmrdkTKEEELRKSGEAKYAHLSDELHVLI 135
Cdd:cd22382     1 RVSDKVMIPQEEYPDINFVGLLIGPRGNTLKKIEKETGAKIMIRGKGS----VKEGKVGRKDGQPLPGEDEPLHALV 73
KH-I_KHDC4_rpt2 cd22386
first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein ...
 59-136 2.18e-10

first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins; KHDC4, also called Brings lots of money 7 (Blom7), or pre-mRNA splicing factor protein KHDC4, is an RNA-binding protein involved in pre-mRNA splicing. It interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome. KHDC4 binds preferentially RNA with A/C rich sequences and poly-C stretches. KHDC4 contains two type I K homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411814 [Multi-domain]  Cd Length: 102  Bit Score: 56.41  E-value: 2.18e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907067540  59 KLSERVLIPVKQYPK-FNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSmrdKTKEEElrkSGEAkyahlSDE-LHVLIE 136
Cdd:cd22386     2 YYQEKVFVGLEHAPPgFNVRGKLIGPGGSNVKHIQQETGAKVQLRGKGS---GFIEPA---SGRE-----ADEpLHLLIS 70
KH smart00322
K homology RNA-binding domain;
59-106 7.13e-06

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 43.05  E-value: 7.13e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1907067540   59 KLSERVLIPVkqypkfNFVGKLLGPRGNSLKRLQEETGAKMSILGKGS 106
Cdd:smart00322   2 PVTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS 43
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 62-106 1.06e-05

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.


Pssm-ID: 411802 [Multi-domain]  Cd Length: 63  Bit Score: 42.29  E-value: 1.06e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1907067540  62 ERVLIPVKqypkfnFVGKLLGPRGNSLKRLQEETGAKMSILGKGS 106
Cdd:cd00105     1 EEIEVPSE------LVGLIIGKGGSTIKEIEEETGARIQIPKEGE 39
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 61-106 1.14e-05

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.


Pssm-ID: 459630 [Multi-domain]  Cd Length: 65  Bit Score: 42.27  E-value: 1.14e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1907067540  61 SERVLIPVKQypkfnfVGKLLGPRGNSLKRLQEETGAKMSILGKGS 106
Cdd:pfam00013   1 TVEILVPSSL------VGLIIGKGGSNIKEIREETGAKIQIPPSES 40
KH-I_IGF2BP2_rpt2 cd22494
second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 67-111 1.98e-03

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.


Pssm-ID: 411922  Cd Length: 77  Bit Score: 36.16  E-value: 1.98e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1907067540  67 PVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSIlgkGSMRDKT 111
Cdd:cd22494     1 PLKILAHNSLVGRLIGKEGRNLKKIEQDTGTKITI---SSLQDLT 42
KH-I_IGF2BP_rpt2 cd22401
second type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 75-101 2.92e-03

second type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.


Pssm-ID: 411829 [Multi-domain]  Cd Length: 72  Bit Score: 35.66  E-value: 2.92e-03
                          10        20
                  ....*....|....*....|....*..
gi 1907067540  75 NFVGKLLGPRGNSLKRLQEETGAKMSI 101
Cdd:cd22401     9 NLCGRLIGKDGRNIKKIMEDTNTKITI 35
KH-I_RIK_like_rpt2 cd22472
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein RIK and ...
 68-106 3.05e-03

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein RIK and similar proteins; RIK, also called rough sheath 2-interacting KH domain protein, or RS2-interacting KH domain protein, is a RNA binding protein that acts together with RS2/AS1 in the recruitment of HIRA. RIK contains two type I K homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411900  Cd Length: 96  Bit Score: 36.27  E-value: 3.05e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1907067540  68 VKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGS 106
Cdd:cd22472    11 IEAPPSFNLAGRIRGPNNSYLQHIASATGATVALRGRGS 49
KH-I_IGF2BP1_rpt2 cd22493
second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 66-101 3.78e-03

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins; IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.


Pssm-ID: 411921  Cd Length: 97  Bit Score: 36.19  E-value: 3.78e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1907067540  66 IPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSI 101
Cdd:cd22493     5 VPLKILAHNNFVGRLIGKEGRNLKKVEQDTETKITI 40
KH-I_NOVA_rpt3 cd09031
third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
 75-105 5.33e-03

third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411807 [Multi-domain]  Cd Length: 71  Bit Score: 34.86  E-value: 5.33e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1907067540  75 NFVGKLLGPRGNSLKRLQEETGAKMSILGKG 105
Cdd:cd09031    10 NLVGAILGKGGKTLVEIQELTGARIQISKKG 40
KH-I_IGF2BP3_rpt2 cd22495
second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 67-101 9.09e-03

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins; IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.


Pssm-ID: 411923  Cd Length: 77  Bit Score: 34.63  E-value: 9.09e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1907067540  67 PVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSI 101
Cdd:cd22495     1 PLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITI 35
KH-I_Vigilin_rpt3 cd22407
third type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 62-101 9.65e-03

third type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the third one.


Pssm-ID: 411835 [Multi-domain]  Cd Length: 62  Bit Score: 34.11  E-value: 9.65e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1907067540  62 ERVLIPVkqypkfNFVGKLLGPRGNSLKRLQEETGAKMSI 101
Cdd:cd22407     2 ERLDIPK------VYHPFIAGPNNENVKELQEETGVRINI 35
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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