NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1958706726|ref|XP_038951689|]
View 

la-related protein 4B isoform X9 [Rattus norvegicus]

Protein Classification

RNA-binding protein( domain architecture ID 10169011)

RNA-binding protein containing an RNA recognition motif (RRM)

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 259-335 6.08e-52

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


The actual alignment was detected with superfamily member cd12706:

Pssm-ID: 473069  Cd Length: 77  Bit Score: 173.70  E-value: 6.08e-52
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958706726 259 CIVILREISESTPVEEVEALFKGDNLPKFINCEFAYNDNWFITFETEADAQQAYKYLREEVRTFQGKPIKARIKAKA 335
Cdd:cd12706     1 CIVILREVPESTPIEEVEALFKGDNLPKFINCEFAYNDNWFITFESEADAQQAYKYLREEVKTFQGKPIKARIKAKA 77
LARP_5 cd08036
La RNA-binding domain of La-related protein 5; This domain is found in vertebrate La-related ...
 180-254 5.24e-44

La RNA-binding domain of La-related protein 5; This domain is found in vertebrate La-related protein 5 (LARP5). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


:

Pssm-ID: 153405  Cd Length: 75  Bit Score: 152.10  E-value: 5.24e-44
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958706726 180 REVLKKTLEFCLSRENLASDMYLISQMDSDQYVPITTVANLDHIKKLSTDVDLIVEVLRSLPLVQVDEKGEKVRP 254
Cdd:cd08036     1 RELLKKTLEFCLSRENLASDMYLISQMDSDQYVPIMTVANLDHIKKLSTDVDLIVDVLRSLPLVQVDEKGEKVRP 75
 
Name Accession Description Interval E-value
RRM_LARP5 cd12706
RNA recognition motif (RRM) found in vertebrate La-related protein 5 (LARP5 or LARP4B); This ...
 259-335 6.08e-52

RNA recognition motif (RRM) found in vertebrate La-related protein 5 (LARP5 or LARP4B); This subgroup corresponds to the RRM of LARP5, a cytosolic protein that co-sediments with polysomes and accumulates upon stress induction in cellular stress granules. It can interact with the cytosolic poly(A) binding protein 1 (PABPC1) and the receptor for activated C Kinase (RACK1), a component of the 40S ribosomal subunit. LARP5 may function as a stimulatory factor of translation through bridging mRNA factors of the 3' end with initiating ribosomes. Like other La-related proteins (LARPs) family members, LARP5 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410105  Cd Length: 77  Bit Score: 173.70  E-value: 6.08e-52
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958706726 259 CIVILREISESTPVEEVEALFKGDNLPKFINCEFAYNDNWFITFETEADAQQAYKYLREEVRTFQGKPIKARIKAKA 335
Cdd:cd12706     1 CIVILREVPESTPIEEVEALFKGDNLPKFINCEFAYNDNWFITFESEADAQQAYKYLREEVKTFQGKPIKARIKAKA 77
LARP_5 cd08036
La RNA-binding domain of La-related protein 5; This domain is found in vertebrate La-related ...
 180-254 5.24e-44

La RNA-binding domain of La-related protein 5; This domain is found in vertebrate La-related protein 5 (LARP5). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153405  Cd Length: 75  Bit Score: 152.10  E-value: 5.24e-44
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958706726 180 REVLKKTLEFCLSRENLASDMYLISQMDSDQYVPITTVANLDHIKKLSTDVDLIVEVLRSLPLVQVDEKGEKVRP 254
Cdd:cd08036     1 RELLKKTLEFCLSRENLASDMYLISQMDSDQYVPIMTVANLDHIKKLSTDVDLIVDVLRSLPLVQVDEKGEKVRP 75
LA smart00715
Domain in the RNA-binding Lupus La protein; unknown function;
177-255 1.95e-32

Domain in the RNA-binding Lupus La protein; unknown function;


Pssm-ID: 128955 [Multi-domain]  Cd Length: 80  Bit Score: 120.03  E-value: 1.95e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958706726  177 EDPREVLKKTLEFCLSRENLASDMYLISQMD-SDQYVPITTVANLDHIKKLSTDVDLIVEVLRSLPLVQVDEKGEKVRPN 255
Cdd:smart00715   1 EELKQKIKKQVEYYFSDENLPRDKFLRKKMDkNDGYVPISTIASFKRVKSLTTDVNLIVEALRSSPKLEVSEDGLKVRRR 80
La pfam05383
La domain; This presumed domain is found at the N-terminus of La RNA-binding proteins as well ...
 183-239 4.48e-18

La domain; This presumed domain is found at the N-terminus of La RNA-binding proteins as well as other proteins. The function of this region is uncertain.


Pssm-ID: 461635  Cd Length: 59  Bit Score: 78.23  E-value: 4.48e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958706726 183 LKKTLEFCLSRENLASDMYLISQMDS--DQYVPITTVANLDHIKKLSTDVDLIVEVLRS 239
Cdd:pfam05383   1 IKKQVEYYFSDENLPKDKFLRKQMDKdpDGYVPISVIASFKRMKKLTTDIDLIAEALRE 59
LHP1 COG5193
La protein, small RNA-binding pol III transcript stabilizing protein and related ...
 154-240 1.44e-03

La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis];


Pssm-ID: 227520 [Multi-domain]  Cd Length: 438  Bit Score: 41.57  E-value: 1.44e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958706726 154 HAEYEPLPE----NSDTGGNESQPESQEDPR-----------EVLKKTLEFCLSRENLASDMYLISQMDSDQYVPITTVA 218
Cdd:COG5193   230 FVEFKYFREaqrfNNGFYRNKKYPNDPETVYyysvepillsiMAKKEQIEYYFSEENLKSDEFLRKKFKKAGFIPLSFIG 309

                          90       100
                  ....*....|....*....|..
gi 1958706726 219 NLDHIKKLSTDVDLIVEVLRSL 240
Cdd:COG5193   310 KFYRNLSFGGDKNLILAAMKEV 331
RRM smart00360
RNA recognition motif;
261-328 1.57e-03

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 37.57  E-value: 1.57e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958706726  261 VILREISESTPVEEVEALFKgdNLPKFINCEFAYNDNW-------FITFETEADAQQAYKYLREevRTFQGKPIK 328
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFS--KFGKVESVRLVRDKETgkskgfaFVEFESEEDAEKALEALNG--KELDGRPLK 72
 
Name Accession Description Interval E-value
RRM_LARP5 cd12706
RNA recognition motif (RRM) found in vertebrate La-related protein 5 (LARP5 or LARP4B); This ...
 259-335 6.08e-52

RNA recognition motif (RRM) found in vertebrate La-related protein 5 (LARP5 or LARP4B); This subgroup corresponds to the RRM of LARP5, a cytosolic protein that co-sediments with polysomes and accumulates upon stress induction in cellular stress granules. It can interact with the cytosolic poly(A) binding protein 1 (PABPC1) and the receptor for activated C Kinase (RACK1), a component of the 40S ribosomal subunit. LARP5 may function as a stimulatory factor of translation through bridging mRNA factors of the 3' end with initiating ribosomes. Like other La-related proteins (LARPs) family members, LARP5 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410105  Cd Length: 77  Bit Score: 173.70  E-value: 6.08e-52
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958706726 259 CIVILREISESTPVEEVEALFKGDNLPKFINCEFAYNDNWFITFETEADAQQAYKYLREEVRTFQGKPIKARIKAKA 335
Cdd:cd12706     1 CIVILREVPESTPIEEVEALFKGDNLPKFINCEFAYNDNWFITFESEADAQQAYKYLREEVKTFQGKPIKARIKAKA 77
RRM_LARP4_5_like cd12430
RNA recognition motif (RRM) found in La-related protein 4 (LARP4), La-related protein 5 (LARP5 ...
 259-334 3.63e-45

RNA recognition motif (RRM) found in La-related protein 4 (LARP4), La-related protein 5 (LARP5 or LARP4B) and similar proteins; This subfamily corresponds to the RRM of LARP4 and LARP5. LARP4 is a cytoplasmic factor that can bind poly(A) RNA and interact with poly(A) binding protein (PABP). It may play a role in promoting translation by stabilizing mRNA. LARP5 is a cytosolic protein that co-sediments with polysomes and accumulates upon stress induction in cellular stress granules. It can interact with the cytosolic poly(A) binding protein 1 (PABPC1) and the receptor for activated C Kinase (RACK1), a component of the 40S ribosomal subunit. LARP5 may function as a stimulatory factor of translation through bridging mRNA factors of the 3' end with initiating ribosomes. Both, LARP4 and LARP5, are structurally related to the La autoantigen. Like other La-related proteins (LARPs) family members, LARP4 and LARP5 contain a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409864 [Multi-domain]  Cd Length: 76  Bit Score: 155.17  E-value: 3.63e-45
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958706726 259 CIVILREISESTPVEEVEALFKGDNLPKFINCEFAYNDNWFITFETEADAQQAYKYLREEVRTFQGKPIKARIKAK 334
Cdd:cd12430     1 CIVILREIPESTPEEEVEALFSGQNCPKFTSCEFAINDSWYVTFESEEDAQEAYKYLREEVKTFNGKPIMARIKAE 76
LARP_5 cd08036
La RNA-binding domain of La-related protein 5; This domain is found in vertebrate La-related ...
 180-254 5.24e-44

La RNA-binding domain of La-related protein 5; This domain is found in vertebrate La-related protein 5 (LARP5). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153405  Cd Length: 75  Bit Score: 152.10  E-value: 5.24e-44
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958706726 180 REVLKKTLEFCLSRENLASDMYLISQMDSDQYVPITTVANLDHIKKLSTDVDLIVEVLRSLPLVQVDEKGEKVRP 254
Cdd:cd08036     1 RELLKKTLEFCLSRENLASDMYLISQMDSDQYVPIMTVANLDHIKKLSTDVDLIVDVLRSLPLVQVDEKGEKVRP 75
LARP_4_5_like cd08031
La RNA-binding domain of proteins similar to La-related proteins 4 and 5; This domain is found ...
 180-254 2.78e-43

La RNA-binding domain of proteins similar to La-related proteins 4 and 5; This domain is found in proteins similar to La-related proteins 4 and 5 (LARP4, LARP5). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153400  Cd Length: 75  Bit Score: 149.90  E-value: 2.78e-43
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958706726 180 REVLKKTLEFCLSRENLASDMYLISQMDSDQYVPITTVANLDHIKKLSTDVDLIVEVLRSLPLVQVDEKGEKVRP 254
Cdd:cd08031     1 KELLKRQLEYYFSRENLANDAYLLSQMDSDQYVPIWTIANFNKIKKLTTDIDLIVEALRESPNVQVDEKGEKVRP 75
RRM_LARP4 cd12707
RNA recognition motif (RRM) found in vertebrate La-related protein 4 (LARP4); This subgroup ...
 259-334 4.45e-40

RNA recognition motif (RRM) found in vertebrate La-related protein 4 (LARP4); This subgroup corresponds to the RRM of LARP4, a cytoplasmic factor that can bind poly(A) RNA and interact with poly(A) binding protein (PABP). It may play a role in promoting translation by stabilizing mRNA. LARP4 is structurally related to the La autoantigen. Like other La-related proteins (LARPs) family members, LARP4 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410106  Cd Length: 77  Bit Score: 141.35  E-value: 4.45e-40
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958706726 259 CIVILREISESTPVEEVEALFKGDNLPKFINCEFAYNDNWFITFETEADAQQAYKYLREEVRTFQGKPIKARIKAK 334
Cdd:cd12707     1 CIIILREIPETTPVEEVKALFKNENCPKVISCEFAHNNNWYITFQSDTDAQQAFKYLREEVKTFQGKPIMARIKAI 76
LARP_4 cd08035
La RNA-binding domain of La-related protein 4; This domain is found in vertebrate La-related ...
 180-254 5.57e-38

La RNA-binding domain of La-related protein 4; This domain is found in vertebrate La-related protein 4 (LARP4), also known as c-MPL binding protein. La-type domains often co-occur with RNA-recognition motifs (RRMs). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153404  Cd Length: 75  Bit Score: 135.56  E-value: 5.57e-38
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958706726 180 REVLKKTLEFCLSRENLASDMYLISQMDSDQYVPITTVANLDHIKKLSTDVDLIVEVLRSLPLVQVDEKGEKVRP 254
Cdd:cd08035     1 RECLKKQLEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEGIKKLTTDMDLILDVLRSSPMVQVDETGEKVRP 75
LA smart00715
Domain in the RNA-binding Lupus La protein; unknown function;
177-255 1.95e-32

Domain in the RNA-binding Lupus La protein; unknown function;


Pssm-ID: 128955 [Multi-domain]  Cd Length: 80  Bit Score: 120.03  E-value: 1.95e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958706726  177 EDPREVLKKTLEFCLSRENLASDMYLISQMD-SDQYVPITTVANLDHIKKLSTDVDLIVEVLRSLPLVQVDEKGEKVRPN 255
Cdd:smart00715   1 EELKQKIKKQVEYYFSDENLPRDKFLRKKMDkNDGYVPISTIASFKRVKSLTTDVNLIVEALRSSPKLEVSEDGLKVRRR 80
LAM cd07323
LA motif RNA-binding domain; This domain is found at the N-terminus of La RNA-binding proteins ...
 180-254 4.47e-25

LA motif RNA-binding domain; This domain is found at the N-terminus of La RNA-binding proteins as well as in other related proteins. Typically, the domain co-occurs with an RNA-recognition motif (RRM), and together these domains function to bind primary transcripts of RNA polymerase III in the La autoantigen (Lupus La protein, LARP3, or Sjoegren syndrome type B antigen, SS-B). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153396  Cd Length: 75  Bit Score: 98.76  E-value: 4.47e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958706726 180 REVLKKTLEFCLSRENLASDMYLISQMDSDQYVPITTVANLDHIKKLSTDVDLIVEVLRSLPLVQVDEKGEKVRP 254
Cdd:cd07323     1 LEKIKKQVEYYFSDENLCKDRFLRSLMDDDGWVPLSLLASFNRVKKLTTDVELILEALRDSSVVEVSEDGTKVRR 75
La pfam05383
La domain; This presumed domain is found at the N-terminus of La RNA-binding proteins as well ...
 183-239 4.48e-18

La domain; This presumed domain is found at the N-terminus of La RNA-binding proteins as well as other proteins. The function of this region is uncertain.


Pssm-ID: 461635  Cd Length: 59  Bit Score: 78.23  E-value: 4.48e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958706726 183 LKKTLEFCLSRENLASDMYLISQMDS--DQYVPITTVANLDHIKKLSTDVDLIVEVLRS 239
Cdd:pfam05383   1 IKKQVEYYFSDENLPKDKFLRKQMDKdpDGYVPISVIASFKRMKKLTTDIDLIAEALRE 59
LARP_1_2 cd08034
La RNA-binding domain proteins similar to La-related proteins 1 and 2; This domain is found in ...
 180-253 1.25e-12

La RNA-binding domain proteins similar to La-related proteins 1 and 2; This domain is found in proteins similar to vertebrate La-related proteins 1 and 2 (LARP1, LARP2). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153403  Cd Length: 73  Bit Score: 63.60  E-value: 1.25e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958706726 180 REVLKKTLEFCLSRENLASDMYLISQMDSDQYVPITTVANLDHIKKLSTDVDLIVEVLRSLPLVQVDekGEKVR 253
Cdd:cd08034     1 KEYIKKQIEYYFSVDNLEKDFFLRRKMDPEGYLPIALIASFHRVQALTTDVNLILEALKDSTVVELV--DEKVR 72
LARP_6 cd08033
La RNA-binding domain of La-related protein 6; This domain is found in animal and plant ...
 183-253 3.36e-11

La RNA-binding domain of La-related protein 6; This domain is found in animal and plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153402  Cd Length: 77  Bit Score: 59.60  E-value: 3.36e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958706726 183 LKKTLEFCLSRENLASDMYLISQM--DSDQYVPITTVANLDHIKKLSTDVDLIVEVLRSLPLVQVDEKGEKVR 253
Cdd:cd08033     4 IVKQVEYYFSDENLLKDAFLLKHVrrNKEGYVPIKLIASFKKVKALTRDWRVVAAALRRSSKLVVSEDGKKVR 76
LARP_2 cd08038
La RNA-binding domain of La-related protein 2; This domain is found in vertebrate La-related ...
 180-248 3.62e-10

La RNA-binding domain of La-related protein 2; This domain is found in vertebrate La-related protein 2 (LARP2). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153407  Cd Length: 73  Bit Score: 56.50  E-value: 3.62e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958706726 180 REVLKKTLEFCLSRENLASDMYLISQMDSDQYVPITTVANLDHIKKLSTDVDLIVEVLR-SLPLVQVDEK 248
Cdd:cd08038     1 KEYIKRQIEYYFSTENLERDFFLRRKMDLQGFLPISLIAGFYRVQALTTNVDLILEALKdSTEVEIVDQK 70
LARP_1 cd08037
La RNA-binding domain of La-related protein 1; This domain is found in vertebrate La-related ...
 180-248 7.28e-10

La RNA-binding domain of La-related protein 1; This domain is found in vertebrate La-related protein 1 (LARP1). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153406  Cd Length: 73  Bit Score: 55.68  E-value: 7.28e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958706726 180 REVLKKTLEFCLSRENLASDMYLISQMDSDQYVPITTVANLDHIKKLSTDVDLIVEVLRSLPLVQ-VDEK 248
Cdd:cd08037     1 KDYIKRQIEYYFSVDNLERDFFLRRKMDEDGFLPVTLIASFHRVQALTTDISLIIKALKDSKVVEiIDMK 70
LA_like_fungal cd08029
La-motif domain of fungal proteins similar to the La autoantigen; This domain is found in ...
 179-253 7.17e-09

La-motif domain of fungal proteins similar to the La autoantigen; This domain is found in fungal proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153398  Cd Length: 76  Bit Score: 52.69  E-value: 7.17e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958706726 179 PREVLKKtLEFCLSRENLASDMYL--ISQMDSDQYVPITTVANLDHIKKLsTDVDLIVEVLRSLPLVQVDEKGEKVR 253
Cdd:cd08029     1 PEEIRKQ-VEFYFSDSNLPTDKFLwtLTGGSNNGWVPIKTIASFKRMRRF-QPLEAVVEALRESELLEVSEDGENVR 75
LARP_7 cd08032
La RNA-binding domain of La-related protein 7; LARP7 is a component of the 7SK snRNP, a key ...
 183-253 4.80e-08

La RNA-binding domain of La-related protein 7; LARP7 is a component of the 7SK snRNP, a key factor in the regulation of RNA polymerase II transcription. 7SK functionality is dependent on the presence of LARP7, which is thought to stabilize the 7SK RNA by interacting with its 3' end. The release of 7SK RNA from P-TEFb/HEXIM/7SK complexes activates the cyclin-dependent kinase P-TEFb, which in turn phosphorylates the C-terminal domain of RNA pol II and mediates a transition into productive transcription elongation.


Pssm-ID: 153401  Cd Length: 82  Bit Score: 50.71  E-value: 4.80e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958706726 183 LKKTLEFCLSRENLASDMYLISQMDS--DQYVPITTVANLDHIKKLSTDVDLIVEVLRSLPLVQVDEKGEKVR 253
Cdd:cd08032     9 IAKQVDFWFGDVNLHKDRFLREQIEKsrDGYIDISLLVSFNKMKKLTTDGKLIARALKNSSVVELNLEGTRIR 81
LARP_3 cd08028
La RNA-binding domain of La-related protein 3; This domain is found at the N-terminus of the ...
 183-253 3.99e-07

La RNA-binding domain of La-related protein 3; This domain is found at the N-terminus of the La autoantigen and similar proteins, and co-occurs with an RNA-recognition motif (RRM). Together these domains function to bind primary transcripts of RNA polymerase III at their 3' terminus and protect them from exonucleolytic degradation. Binding is specific for the 3'-terminal UUU-OH motif. The La autoantigen is also called Lupus La protein, LARP3, or Sjoegren syndrome type B antigen (SS-B).


Pssm-ID: 153397  Cd Length: 82  Bit Score: 48.06  E-value: 3.99e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958706726 183 LKKTLEFCLSRENLASDMYLISQM-DSDQYVPITTVANLDHIKKLSTDVDLIVEVLR--SLPLVQVDEKGEKVR 253
Cdd:cd08028     8 IIRQIEYYFGDFNLPRDKFLKEQIkEDDGWVPMEVMLKFNRLKSLSSDPEVIAKALKksKSGLIEVSEDKTKIR 81
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 261-330 1.12e-04

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 40.73  E-value: 1.12e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958706726 261 VILREISESTPVEEVEALFKgdNLPKFINCEFAYNDNW------FITFETEADAQQAYKYLREevRTFQGKPIKAR 330
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFS--KFGEVVSVRIVRDRDGkskgfaFVEFESPEDAEKALEALNG--TELGGRPLKVS 72
LHP1 COG5193
La protein, small RNA-binding pol III transcript stabilizing protein and related ...
 154-240 1.44e-03

La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis];


Pssm-ID: 227520 [Multi-domain]  Cd Length: 438  Bit Score: 41.57  E-value: 1.44e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958706726 154 HAEYEPLPE----NSDTGGNESQPESQEDPR-----------EVLKKTLEFCLSRENLASDMYLISQMDSDQYVPITTVA 218
Cdd:COG5193   230 FVEFKYFREaqrfNNGFYRNKKYPNDPETVYyysvepillsiMAKKEQIEYYFSEENLKSDEFLRKKFKKAGFIPLSFIG 309

                          90       100
                  ....*....|....*....|..
gi 1958706726 219 NLDHIKKLSTDVDLIVEVLRSL 240
Cdd:COG5193   310 KFYRNLSFGGDKNLILAAMKEV 331
RRM smart00360
RNA recognition motif;
261-328 1.57e-03

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 37.57  E-value: 1.57e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958706726  261 VILREISESTPVEEVEALFKgdNLPKFINCEFAYNDNW-------FITFETEADAQQAYKYLREevRTFQGKPIK 328
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFS--KFGKVESVRLVRDKETgkskgfaFVEFESEEDAEKALEALNG--KELDGRPLK 72
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH