NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|164565405|ref|NP_766293|]
View 

PHD finger protein 13 [Mus musculus]

Protein Classification

PHD finger protein 13( domain architecture ID 10204328)

PHD finger protein 13 (PHF13) is required for normal chromosome condensation during the early stages of mitosis

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
PHD_PHF13 cd15632
PHD finger found in PHD finger protein 13 (PHF13); PHF13, also termed survival time-associated ...
228-274 5.80e-31

PHD finger found in PHD finger protein 13 (PHF13); PHF13, also termed survival time-associated PHD finger protein in ovarian cancer 1 (SPOC1), is a novel plant homeodomain (PHD) finger-containing protein that shows strong expression in spermatogonia and ovarian cancer cells, modulates chromatin structure and mitotic chromosome condensation, and is important for proper cell division. It is also required for spermatogonial stem cell differentiation and sustained spermatogenesis. The overexpression of PHF13 associates with unresectable carcinomas and shorter survival in ovarian cancer.


:

Pssm-ID: 277102  Cd Length: 47  Bit Score: 110.13  E-value: 5.80e-31
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 164565405 228 LVTCFCMKPFAGRPMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCR 274
Cdd:cd15632    1 LVTCFCMKPFAGRPMIECNECHTWIHLSCAKIRKSNVPEVYVCQKCR 47
 
Name Accession Description Interval E-value
PHD_PHF13 cd15632
PHD finger found in PHD finger protein 13 (PHF13); PHF13, also termed survival time-associated ...
228-274 5.80e-31

PHD finger found in PHD finger protein 13 (PHF13); PHF13, also termed survival time-associated PHD finger protein in ovarian cancer 1 (SPOC1), is a novel plant homeodomain (PHD) finger-containing protein that shows strong expression in spermatogonia and ovarian cancer cells, modulates chromatin structure and mitotic chromosome condensation, and is important for proper cell division. It is also required for spermatogonial stem cell differentiation and sustained spermatogenesis. The overexpression of PHF13 associates with unresectable carcinomas and shorter survival in ovarian cancer.


Pssm-ID: 277102  Cd Length: 47  Bit Score: 110.13  E-value: 5.80e-31
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 164565405 228 LVTCFCMKPFAGRPMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCR 274
Cdd:cd15632    1 LVTCFCMKPFAGRPMIECNECHTWIHLSCAKIRKSNVPEVYVCQKCR 47
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
231-273 4.87e-04

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 37.19  E-value: 4.87e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 164565405   231 CFCMKPFAGRPMIECNECHTWIHLSCAKI--RKSNVPEVFVCQKC 273
Cdd:smart00249   3 SVCGKPDDGGELLQCDGCDRWYHQTCLGPplLEEEPDGKWYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
231-274 1.38e-03

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 35.93  E-value: 1.38e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 164565405  231 CFCMKPFAGRPMIECNECHTWIHLSCAKIRKSNVP---EVFVCQKCR 274
Cdd:pfam00628   3 AVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPAEipsGEWLCPECK 49
 
Name Accession Description Interval E-value
PHD_PHF13 cd15632
PHD finger found in PHD finger protein 13 (PHF13); PHF13, also termed survival time-associated ...
228-274 5.80e-31

PHD finger found in PHD finger protein 13 (PHF13); PHF13, also termed survival time-associated PHD finger protein in ovarian cancer 1 (SPOC1), is a novel plant homeodomain (PHD) finger-containing protein that shows strong expression in spermatogonia and ovarian cancer cells, modulates chromatin structure and mitotic chromosome condensation, and is important for proper cell division. It is also required for spermatogonial stem cell differentiation and sustained spermatogenesis. The overexpression of PHF13 associates with unresectable carcinomas and shorter survival in ovarian cancer.


Pssm-ID: 277102  Cd Length: 47  Bit Score: 110.13  E-value: 5.80e-31
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 164565405 228 LVTCFCMKPFAGRPMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCR 274
Cdd:cd15632    1 LVTCFCMKPFAGRPMIECNECHTWIHLSCAKIRKSNVPEVYVCQKCR 47
PHD_PHF13_like cd15546
PHD finger found in PHD finger proteins PHF13 and PHF23; PHF13, also termed survival ...
230-273 1.02e-27

PHD finger found in PHD finger proteins PHF13 and PHF23; PHF13, also termed survival time-associated PHD finger protein in ovarian cancer 1 (SPOC1), is a novel plant homeodomain (PHD) finger-containing protein that shows strong expression in spermatogonia and ovarian cancer cells, modulates chromatin structure and mitotic chromosome condensation, and is important for proper cell division. It is also required for spermatogonial stem cell differentiation and sustained spermatogenesis. The overexpression of PHF13 associates with unresectable carcinomas and shorter survival in ovarian cancer. PHF23, also termed PHD-containing protein JUNE-1, is a hypothetical protein with a PHD finger. It is encoded by gene PHF23 that acts as a candidate fusion partner for the nucleoporin gene NUP98. The NUP98-PHF23 fusion results from a cryptic translocation t(11;17)(p15;p13) in acute myeloid leukemia (AML).


Pssm-ID: 277021  Cd Length: 44  Bit Score: 101.37  E-value: 1.02e-27
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 164565405 230 TCFCMKPFAGRPMIECNECHTWIHLSCAKIRKSNVPEVFVCQKC 273
Cdd:cd15546    1 TCFCGKPFAGRPMIECSECLTWIHLSCAKIRKNNVPEVFICQKC 44
PHD_PHF23 cd15631
PHD finger found in PHD finger protein 23 (PHF23); PHF23, also termed PHD-containing protein ...
230-273 9.38e-24

PHD finger found in PHD finger protein 23 (PHF23); PHF23, also termed PHD-containing protein JUNE-1, is a hypothetical protein with a plant homeodomain (PHD) finger. It is encoded by gene PHF23 that acts as a candidate fusion partner for the nucleoporin gene NUP98. The NUP98-PHF23 fusion results from a cryptic translocation t(11;17)(p15;p13) in acute myeloid leukemia (AML).


Pssm-ID: 277101  Cd Length: 44  Bit Score: 91.13  E-value: 9.38e-24
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 164565405 230 TCFCMKPFAGRPMIECNECHTWIHLSCAKIRKSNVPEVFVCQKC 273
Cdd:cd15631    1 TCYCGKPFAGRPMIECSQCGTWIHLSCAKIKKSNVPDFFYCQKC 44
PHD_Ecm5p_Lid2p_like cd15518
PHD finger found in Saccharomyces cerevisiae extracellular matrix protein 5 (Ecm5p), ...
231-273 3.41e-06

PHD finger found in Saccharomyces cerevisiae extracellular matrix protein 5 (Ecm5p), Schizosaccharomyces pombe Lid2 complex component Lid2p, and similar proteins; The family includes Saccharomyces cerevisiae Ecm5p, Schizosaccharomyces pombe Lid2 complex component Lid2p, and similar proteins. Ecm5p is a JmjC domain-containing protein that directly removes histone lysine methylation via a hydroxylation reaction. It associates with the yeast Snt2p and Rpd3 deacetylase, which may play a role in regulating transcription in response to oxidative stress. Ecm5p promotes oxidative stress tolerance, while Snt2p ultimately decreases tolerance. Ecm5p contains an N-terminal ARID domain, a JmjC domain, and a C-terminal plant homeodomain (PHD) finger. Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model includes the second PHD finger of Lid2p.


Pssm-ID: 276993  Cd Length: 45  Bit Score: 43.11  E-value: 3.41e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 164565405 231 CFCMKPFAGRpMIECNECHTWIHLSCAKIRKSNVPE--VFVCQKC 273
Cdd:cd15518    2 CFCRQGEGGT-MIECEICKEWYHVKCIKNGRWKLDDddKFVCPIC 45
PHD_PHF20L1 cd15633
PHD finger found in PHD finger protein 20-like protein 1 (P20L1); P20L1 is an active malignant ...
242-275 3.75e-05

PHD finger found in PHD finger protein 20-like protein 1 (P20L1); P20L1 is an active malignant brain tumor (MBT) domain-containing protein that binds to monomethylated lysine 142 on DNA (Cytosine-5) Methyltransferase 1 (DNMT1) (DNMT1K142me1) and colocalizes at the perinucleolar space in a SET7-dependent manner. Its MBT domain reads and controls enzyme levels of methylated DNMT1 in cells, thus representing a novel antagonist of DNMT1 proteasomal degradation. In addition to the MBT domain, PHF20L1 also contains two Tudor domains, a plant homeodomain (PHD) finger and the putative DNA-binding domains, AT hook and Cys2His2-type zinc finger.


Pssm-ID: 277103  Cd Length: 46  Bit Score: 40.39  E-value: 3.75e-05
                         10        20        30
                 ....*....|....*....|....*....|....
gi 164565405 242 MIECNECHTWIHLSCAKIRKSNVPEVFVCQKCRD 275
Cdd:cd15633   13 MIQCEECLCWQHSVCMGLLEESIPEQYICYICRD 46
PHD_PHF3_like cd15552
PHD finger found in PHD finger protein 3 (PHF3), and death-inducer obliterator variants Dido1, ...
231-273 3.95e-05

PHD finger found in PHD finger protein 3 (PHF3), and death-inducer obliterator variants Dido1, Dido2, and Dido3; PHF3 is a human homolog of yeast protein bypass of Ess1 (Bye1), a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. PHF3 contains an N-terminal plant homeodomain (PHD) finger, a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain. This family also includes Dido gene encoding three alternative splicing variants (Dido1, 2, and 3), which have been implicated in a number of cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. Dido1 is important for maintaining embryonic stem (ES) cells and directly regulates the expression of pluripotency factors. It is the shortest isoform that contains only a highly conserved PHD finger responsible for the binding of histone H3 with a higher affinity for trimethylated lysine4 (H3K4me3). Gene Dido1 is a Bone morphogenetic protein (BMP) target gene and promotes BMP-induced melanoma progression. It also triggers apoptosis after nuclear translocation and caspase upregulation. Dido3 is the largest isoform and is ubiquitously expressed in all human tissues. It is dispensable for ES cell self-renewal and pluripotency, but is involved in the maintenance of stem cell genomic stability and tumorigenesis. Dido3 contains a PHD finger, a transcription elongation factor S-II subunit M (TFSIIM) domain, a SPOC module, and a long C-terminal region (CT) of unknown homology.


Pssm-ID: 277027  Cd Length: 50  Bit Score: 40.46  E-value: 3.95e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 164565405 231 CFCMKPFAGRPMIECNECHTWIHLSCAKIRKSNVPEV------FVCQKC 273
Cdd:cd15552    2 CICRKPHNNRFMICCDRCEEWFHGDCVGITEAQGKEMeenieeYVCPKC 50
PHD_PHF2_like cd15554
PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar ...
231-273 2.33e-04

PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar proteins. PHF2, also termed GRC5, or PHD finger protein 2, is a histone lysine demethylase ubiquitously expressed in various tissues. PHF8, also termed PHD finger protein 8, or KDM7B, is a monomethylated histone H4 lysine 20(H4K20me1) demethylase that transcriptionally regulates many cell cycle genes. It also preferentially acts on H3K9me2 and H3K9me1. PHF8 is modulated by CDC20-containing anaphase-promoting complex (APC (cdc20)) and plays an important role in the G2/M transition. It acts as a critical molecular sensor for mediating retinoic acid (RA) treatment response in RAR alpha-fusion-induced leukemia. Moreover, PHF8 is essential for cytoskeleton dynamics and is associated with X-linked mental retardation. KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. All family members contain a plant homeodomain (PHD) finger and a JmjC domain.


Pssm-ID: 277029  Cd Length: 47  Bit Score: 38.13  E-value: 2.33e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 164565405 231 CFCMKPF-AGRPMIECNECHTWIHLSCAKIRK--SNVPEVFVCQKC 273
Cdd:cd15554    2 CICRQPYdVTRFMIECDVCKDWFHGSCVGVEEhqANDIERYHCPNC 47
PHD_Bye1p_SIZ1_like cd15570
PHD domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p), the E3 Sumo ...
231-273 2.51e-04

PHD domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p), the E3 Sumo Ligase SIZ1, and similar proteins; Yeast Bye1p is a nuclear transcription factor with a domain resembling the central domain in the transcription elongation factor TFIIS and plays an inhibitory role during transcription elongation. It functions as a multicopy suppressor of Ess1, a peptidyl-prolyl cis-trans isomerase involved in proline isomerization of the C-terminal domain (CTD) of RNA polymerase II (Pol II). Bye1p contains an N-terminal plant homeodomain (PHD) finger, a central Pol II-binding TFIIS-like domain (TLD) domain, and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain. The PHD domain binds to a histone H3 tail peptide containing trimethylated lysine 4 (H3K4me3). The TLD domain is responsible for the association with chromatin. Plant SIZ1 protein is a SUMO (small ubiquitin-related modifier) E3 ligase that facilitates conjugation of SUMO to substrate target proteins (sumoylation) and belongs to the protein inhibitor of activated STAT (PIAS) protein family. It negatively regulates abscisic acid (ABA) signaling, which is dependent on the bZIP transcripton factor ABI5. It also modulates plant growth and plays a role in drought stress response likely through the regulation of gene expression. SIZ1 functions as a floral repressor that not only represses the salicylic acid (SA)-dependent pathway, but also promotes FLOWERING LOCUS C (FLC) expression by repressing FLOWERING LOCUS D (FLD) activity through sumoylation. SIZ1 contains a PHD finger, which specifically binds methylated histone H3 at lysine 4 and arginine 2.


Pssm-ID: 277045  Cd Length: 50  Bit Score: 38.21  E-value: 2.51e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 164565405 231 CFCMKPFAGRPMIECNECHTWIHLSCAKIRKS------NVPEVFVCQKC 273
Cdd:cd15570    2 CPCGSSMEDGSMIQCEGCKTWQHMDCVLIPDKpadglpELPSKFYCELC 50
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
231-273 4.87e-04

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 37.19  E-value: 4.87e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 164565405   231 CFCMKPFAGRPMIECNECHTWIHLSCAKI--RKSNVPEVFVCQKC 273
Cdd:smart00249   3 SVCGKPDDGGELLQCDGCDRWYHQTCLGPplLEEEPDGKWYCPKC 47
PHD_KDM7 cd15640
PHD finger found in lysine-specific demethylase 7 (KDM7); KDM7, also termed JmjC ...
231-273 4.87e-04

PHD finger found in lysine-specific demethylase 7 (KDM7); KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. KDM7 contains a plant homeodomain (PHD) that binds Lys4-trimethylated histone 3 (H3K4me3) and a jumonji domain that demethylates either H3K9me2 or H3K27me2.


Pssm-ID: 277110  Cd Length: 50  Bit Score: 37.27  E-value: 4.87e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 164565405 231 CFCMKPF-AGRPMIECNECHTWIHLSCAKIRKSNVPEV--FVCQKC 273
Cdd:cd15640    2 CVCRQPYdVNRFMIECDICKDWFHGSCVQVEEHHAADIdlYHCPNC 47
PHD_SPP1 cd16039
PHD finger found in Set1 complex component SPP1; Set1C component SPP1, also called COMPASS ...
231-273 5.44e-04

PHD finger found in Set1 complex component SPP1; Set1C component SPP1, also called COMPASS component Spp1, or Complex proteins associated with set1 protein Spp1, or Suppressor of PRP protein 1, is a component of the COMPASS complex that links histone methylation to initiation of meiotic recombination. It induces double-strand break (DSB) formation by tethering to recombinationally cold regions. SPP1 interacts with H3K4me3 and Mer2, a protein required for DSB formation, to promote recruitment of potential meiotic DSB sites to the chromosomal axis. SPP1 contains a PHD finger, a zinc binding motif.


Pssm-ID: 277186  Cd Length: 46  Bit Score: 37.07  E-value: 5.44e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 164565405 231 CFCMKPFAGRPMIECNECHTWIHLSCAKIRKSNVPEV--FVCQKC 273
Cdd:cd16039    2 CICQKPDDGRWMIACDGCDEWYHFTCVNIPEADVELVdsFFCPPC 46
PHD_PHF20 cd15634
PHD finger found in PHD finger protein 20 (PHF20); PHF20, also termed Glioma-expressed antigen ...
231-273 5.89e-04

PHD finger found in PHD finger protein 20 (PHF20); PHF20, also termed Glioma-expressed antigen 2, or hepatocellular carcinoma-associated antigen 58, or novel zinc finger protein, or transcription factor TZP (referring to Tudor and zinc finger domain containing protein), is a regulator of NF-kappaB activation by disrupting recruitment of PP2A to p65. It also functions as a transcription factor that binds Akt and plays a role in Akt cell survival/growth signaling. Moreover, it transcriptionally regulates p53. The phosphorylation of PHF20 on Ser291 mediated by protein kinase B (PKB) is essential in tumorigenesis via the regulation of p53 mediated signaling. PHF20 contains an N-terminal malignant brain tumor (MBT) domain, two Tudor domains, a plant homeodomain (PHD) finger and the putative DNA-binding domains, AT hook and Cys2His2-type zinc finger.


Pssm-ID: 277104  Cd Length: 44  Bit Score: 36.85  E-value: 5.89e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 164565405 231 CFCMKPFAGRPMIECNECHTWIHLSCAKIRKSNVPEVFVCQKC 273
Cdd:cd15634    2 CICEVQEENDFMIQCEECLCWQHGVCMGLLEDNVPEKYTCYIC 44
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
231-273 7.07e-04

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 36.91  E-value: 7.07e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 164565405 231 CFCMKPF-AGRPMIECNECHTWIHLSCAKI--RKSNVPEVFVCQKC 273
Cdd:cd15489    3 IVCGKGGdLGGELLQCDGCGKWFHADCLGPplSSFVPNGKWICPVC 48
PHD_Cfp1 cd15553
PHD finger found in CXXC-type zinc finger protein 1 (Cfp1); Cfp1, also termed CpG-binding ...
231-273 1.28e-03

PHD finger found in CXXC-type zinc finger protein 1 (Cfp1); Cfp1, also termed CpG-binding protein, or PHD finger and CXXC domain-containing protein 1 (PCCX1), is a specificity factor that binds to unmethylated CpGs and links H3K4me3 with CpG islands (CGIs). It integrates both promoter CpG content and gene activity for accurate trimethylation of histone H3 Lys 4 (H3K4me3) deposition in embryonic stem cells. Moreover, Cfp1 is an essential component of the SETD1 histone H3K4 methyltransferase complex and functions as a critical regulator of histone methylation, cytosine methylation, cellular differentiation, and vertebrate development. Cfp1 contains a plant homeodomain (PHD) finger, a CXXC domain, and a CpG binding protein zinc finger C-terminal domain. Its CXXC domain selectively binds to non-methylated CpG islands, following by a preference for a guanosine nucleotide.


Pssm-ID: 277028  Cd Length: 46  Bit Score: 36.20  E-value: 1.28e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 164565405 231 CFCMKPFAGRPMIECNECHTWIHLSCAKIRKSNVPEV--FVCQKC 273
Cdd:cd15553    2 CICRSSDISRFMIGCDNCEEWYHGDCINITEKEAKAIkeWYCQQC 46
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
233-273 1.30e-03

PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, transcription initiation factor TFIID 140 kDa subunit (TAF140), or TAFII-140, is an integral component of TFIID) is a general initiation factor (GTF) that plays a key role in preinitiation complex (PIC) assembly through core promoter recognition. The interaction of H3K4me3 with TAF3 directs global TFIID recruitment to active genes, which regulates gene-selective functions of p53 in response to genotoxic stress. TAF3 is highly enriched in embryonic stem cells and is required for endoderm lineage differentiation and prevents premature specification of neuroectoderm and mesoderm. Moreover, TAF3, along with TRF3, forms a complex that is essential for myogenic differentiation. TAF3 contains a plant homeodomain (PHD) finger. This family also includes Drosophila melanogaster BIP2 (Bric-a-brac interacting protein 2) protein, which functions as an interacting partner of D. melanogaster p53 (Dmp53).


Pssm-ID: 276997 [Multi-domain]  Cd Length: 46  Bit Score: 36.11  E-value: 1.30e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 164565405 233 CMKPFAGRPMIECNECHTWIHLSCAKIRKSNVPEV-FVCQKC 273
Cdd:cd15522    5 CKKPDDGSPMIGCDECDDWYHWECVGITDEPPEEDdWFCPKC 46
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
231-274 1.38e-03

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 35.93  E-value: 1.38e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 164565405  231 CFCMKPFAGRPMIECNECHTWIHLSCAKIRKSNVP---EVFVCQKCR 274
Cdd:pfam00628   3 AVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPAEipsGEWLCPECK 49
PHD_PHF20_like cd15549
PHD finger found in PHD finger protein 20 (PHF20) and PHD finger protein 20-like protein 1 ...
231-273 1.41e-03

PHD finger found in PHD finger protein 20 (PHF20) and PHD finger protein 20-like protein 1 (P20L1); PHF20, also termed Glioma-expressed antigen 2, or hepatocellular carcinoma-associated antigen 58, or novel zinc finger protein, or transcription factor TZP (referring to Tudor and zinc finger domain containing protein), is a regulator of NF-kappaB activation by disrupting recruitment of PP2A to p65. It also functions as a transcription factor that binds Akt and plays a role in Akt cell survival/growth signaling. Moreover, it transcriptionally regulates p53. The phosphorylation of PHF20 on Ser291 mediated by protein kinase B (PKB) is essential in tumorigenesis via the regulation of p53 mediated signaling. P20L1 is an active malignant brain tumor (MBT) domain-containing protein that binds to monomethylated lysine 142 on DNA (Cytosine-5) Methyltransferase 1 (DNMT1) (DNMT1K142me1) and colocalizes at the perinucleolar space in a SET7-dependent manner. Its MBT domain reads and controls enzyme levels of methylated DNMT1 in cells, thus representing a novel antagonist of DNMT1 proteasomal degradation. Both PHF20 and PHF20L1 contain an N-terminal MBT domain, two Tudor domains, a plant homeodomain (PHD) finger and the putative DNA-binding domains, AT hook and Cys2His2-type zinc finger.


Pssm-ID: 277024  Cd Length: 45  Bit Score: 35.91  E-value: 1.41e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 164565405 231 CFCMKPFAGRPMIECNECHTWIHLSCAKI-RKSNVPEVFVCQKC 273
Cdd:cd15549    2 CICGVNEENGLMIQCELCLCWQHGVCMGIeEEESVPERYVCYVC 45
PHD_MMD1_like cd15556
PHD finger found in Arabidopsis thaliana PHD finger protein MALE MEIOCYTE DEATH 1 (MMD1), PHD ...
239-273 1.74e-03

PHD finger found in Arabidopsis thaliana PHD finger protein MALE MEIOCYTE DEATH 1 (MMD1), PHD finger protein MALE STERILITY 1 (MS1), and similar proteins; MMD1 is a plant homeodomain (PHD) finger protein expressed in male meiocytes. It is encoded by the gene DUET, which is required for male meiotic chromosome organization and progression. MMD1 has been implicated in the regulation of gene expression during meiosis. The mmd1 mutation triggers cell death in male meiocytes. MS1 is a nuclear transcriptional activator that is important for tapetal development and pollen wall biosynthesis. It contains a Leu zipper-like domain and a PHD finger motif, both of which are essential for its function.


Pssm-ID: 277031 [Multi-domain]  Cd Length: 46  Bit Score: 35.82  E-value: 1.74e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 164565405 239 GRPMIECNECHTWIHLSCAKIRKS-NVPEVFVCQKC 273
Cdd:cd15556   11 GERMIACDVCEVWQHTRCVGIADNeEPPDHFLCRRC 46
PHD_MLL5 cd15550
PHD finger found in mixed lineage leukemia 5 (MLL5); MLL5 is a histone methyltransferase that ...
230-273 2.11e-03

PHD finger found in mixed lineage leukemia 5 (MLL5); MLL5 is a histone methyltransferase that plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. It contains a single plant homeodomain (PHD) finger followed by a catalytic SET domain. MLL5 can be recruited to E2F1-responsive promoters to stimulate H3K4 trimethylation and transcriptional activation by binding to the cell cycle regulator host cell factor (HCF-1), thereby facilitating the cell cycle G1 to S phase transition. It is also involved in mitotic fidelity and genomic integrity by modulating the stability of the chromosomal passenger complex (CPC) via the interaction with Borealin. Moreover, MLL5 is a component of a complex associated with retinoic acid receptor that requires GlcN Acylation of its SET domain in order to activate its histone lysine methyltransferase activity. It also participates in the camptothecin (CPT)-induced p53 activation. Furthermore, MLL5 indirectly regulates H3K4 methylation, represses cyclin A2 (CycA) expression, and promotes myogenic differentiation.


Pssm-ID: 277025 [Multi-domain]  Cd Length: 44  Bit Score: 35.37  E-value: 2.11e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 164565405 230 TCFCMKPFAGRPMIECNECHTWIHLSCAKIRKSNVPEVFVCQKC 273
Cdd:cd15550    1 RCICGFEHDDGFMICCDKCSVWQHGDCMGIDRENIPDSYLCEQC 44
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
243-273 3.46e-03

PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and KDM5B, and other similar proteins; TCF-19 was identified as a putative trans-activating factor with expression beginning at the late G1-S boundary in dividing cells. It functions as a novel islet factor necessary for proliferation and survival in the INS-1 beta cell line. It plays an important role in susceptibility to both Type 1 Diabetes Mellitus (T1DM) and Type 2 Diabetes Mellitus (T2DM); it has been suggested that it may positively impact beta cell mass under conditions of beta cell stress and increased insulin demand. KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interaction with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. This family also includes Caenorhabditis elegans Lysine-specific demethylase 7 homolog (ceKDM7A). ceKDM7A (also termed JmjC domain-containing protein 1.2, PHD finger protein 8 homolog, or PHF8 homolog) is a plant homeodomain (PHD)- and JmjC domain-containing protein that functions as a histone demethylase specific for H3K9me2 and H3K27me2. The binding of the PHD finger to H3K4me3 guides H3K9me2- and H3K27me2-specific demethylation by its catalytic JmjC domain in a trans-histone regulation mechanism. In addition, this family includes plant protein OBERON 1 and OBERON 2, Alfin1-like (AL) proteins, histone acetyltransferases (HATs) HAC, and AT-rich interactive domain-containing protein 4 (ARID4).


Pssm-ID: 276992 [Multi-domain]  Cd Length: 49  Bit Score: 34.83  E-value: 3.46e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 164565405 243 IECNECHTWIHLSCAK--IRKSNVPEVFVCQKC 273
Cdd:cd15517   17 VQCDGCDKWFHQFCLGlsNERYADEDKFKCPNC 49
PHD_Hop1p_like cd15558
PHD finger found in Schizosaccharomyces pombe meiosis-specific protein hop1 (Hop1p) and ...
242-273 3.77e-03

PHD finger found in Schizosaccharomyces pombe meiosis-specific protein hop1 (Hop1p) and similar proteins; Fission yeast Hop1p, also termed linear element-associated protein hop1, is an S. pombe homolog of the synaptonemal complex (SC)-associated protein Hop1 in Saccharomyces cerevisiae. In contrast to S. cerevisiae, S. pombe forms thin threads, known as linear elements (LinEs), in meiotic nuclei, instead of a canonical synaptonemal complex. LinEs contain Rec10 protein and are evolutionary relics of SC axial elements. Fission yeast Hop1p is a linear element (LinE)-associated protein. It also associates with Rec10, which plays a role in recruiting the recombination machinery to chromatin. Hop1p contains an N-terminal HORMA (for Hop1p, Rev7p, and MAD2) domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277033  Cd Length: 47  Bit Score: 34.73  E-value: 3.77e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 164565405 242 MIECNECHTWIHLSC---AKIRKSNVPEVFVCQKC 273
Cdd:cd15558   13 MIQCAFCDTWQHLLCygfESAKDPRIPDIHVCYRC 47
PHD_ATX3_4_5_like cd15495
PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis ...
237-273 9.53e-03

PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like protein ATX3, ATX4, ATX5, and similar proteins; The family includes A. thaliana ATX3 (also termed protein SET domain group 14, or trithorax-homolog protein 3), ATX4 (also termed protein SET domain group 16, or trithorax-homolog protein 4) and ATX5 (also termed protein SET domain group 29, or trithorax-homolog protein 5), which belong to the histone-lysine methyltransferase family. They show distinct phylogenetic origins from the ATX1 and ATX2 family. They are multi-domain containing proteins that consist of an N-terminal PWWP domain, a canonical Cys4HisCys3 plant homeodomain (PHD) finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a C-terminal SET domain; this model corresponds to the Cys4HisCys3 canonical PHD finger.


Pssm-ID: 276970 [Multi-domain]  Cd Length: 47  Bit Score: 33.50  E-value: 9.53e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 164565405 237 FAGRPMIECNECHTWIHLSCAKIRKSNVPEVFVCQKC 273
Cdd:cd15495   11 DDNNPLITCNRCQISVHQKCYGIREVDPDGSWVCRAC 47
 
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
HHS Vulnerability Disclosure