PRDM5 (PR/SET domain 5) - Rat Genome Database

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Gene: PRDM5 (PR/SET domain 5) Pan paniscus
Analyze
Symbol: PRDM5
Name: PR/SET domain 5
RGD ID: 11881013
Description: ENCODES a protein that exhibits DNA binding (inferred); DNA-binding transcription activator activity, RNA polymerase II-specific (inferred); DNA-binding transcription factor activity (inferred); INVOLVED IN cellular response to leukemia inhibitory factor (ortholog); negative regulation of transcription by RNA polymerase II (ortholog); positive regulation of transcription by RNA polymerase II (ortholog); ASSOCIATED WITH Axenfeld-Rieger syndrome type 1 (ortholog); brittle cornea syndrome 1 (ortholog); brittle cornea syndrome 2 (ortholog); FOUND IN nuclear body (inferred); nucleolus (inferred); nucleoplasm (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: PR domain zinc finger protein 5
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Mhudiblu_PPA_v0 - Bonobo Mhudiblu_PPA_v0 Assembly
Position:
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v23118,476,696 - 118,707,355 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan14118,761,096 - 118,995,386 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v04112,896,606 - 113,127,400 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.14124,036,911 - 124,252,056 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4124,036,911 - 124,252,928 (-)Ensemblpanpan1.1panPan2
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nuclear body  (IEA)
nucleolus  (IEA)
nucleoplasm  (IEA)
nucleus  (IEA)

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
PRDM5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v23118,476,696 - 118,707,355 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan14118,761,096 - 118,995,386 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v04112,896,606 - 113,127,400 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.14124,036,911 - 124,252,056 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4124,036,911 - 124,252,928 (-)Ensemblpanpan1.1panPan2
PRDM5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh384120,684,291 - 120,922,726 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl4120,684,919 - 120,922,870 (-)EnsemblGRCh38hg38GRCh38
GRCh374121,613,070 - 121,843,881 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 364121,835,379 - 122,063,463 (-)NCBINCBI36Build 36hg18NCBI36
Build 344121,973,534 - 122,201,618NCBI
Celera4119,000,898 - 119,228,989 (-)NCBICelera
Cytogenetic Map4q27NCBI
HuRef4117,343,051 - 117,571,126 (-)NCBIHuRef
CHM1_14121,592,306 - 121,820,496 (-)NCBICHM1_1
T2T-CHM13v2.04123,965,980 - 124,226,930 (-)NCBIT2T-CHM13v2.0
Prdm5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39665,754,640 - 65,914,606 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl665,755,972 - 65,913,994 (+)EnsemblGRCm39 Ensembl
GRCm38665,777,656 - 65,937,622 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl665,778,988 - 65,937,010 (+)EnsemblGRCm38mm10GRCm38
MGSCv37665,728,956 - 65,886,371 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36665,708,617 - 65,865,951 (+)NCBIMGSCv36mm8
Celera667,905,125 - 68,063,194 (+)NCBICelera
Cytogenetic Map6C1NCBI
cM Map630.32NCBI
Prdm5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8496,405,492 - 96,567,647 (+)NCBIGRCr8
mRatBN7.2495,075,736 - 95,237,921 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl495,075,768 - 95,238,301 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0496,659,062 - 96,810,816 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl496,659,084 - 96,812,263 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04161,443,531 - 161,604,796 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4495,448,787 - 95,620,031 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera489,805,717 - 89,965,943 (+)NCBICelera
Cytogenetic Map4q31NCBI
Prdm5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542819,714,730 - 19,881,917 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542819,684,721 - 19,881,716 (+)NCBIChiLan1.0ChiLan1.0
PRDM5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11919,129,418 - 19,327,377 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1919,129,081 - 19,325,590 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1919,352,083 - 19,548,712 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01919,256,009 - 19,455,852 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.11919,214,952 - 19,414,721 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01919,486,468 - 19,686,537 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01919,965,407 - 20,165,939 (+)NCBIUU_Cfam_GSD_1.0
Prdm5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530166,595,007 - 66,730,445 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936662390,894 - 516,485 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936662388,279 - 524,803 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRDM5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8103,189,561 - 103,382,094 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.18103,188,312 - 103,383,955 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28110,658,856 - 110,852,557 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PRDM5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1767,985,387 - 68,207,113 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl767,987,359 - 68,206,893 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603746,952,855 - 47,174,019 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Prdm5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624777676,965 - 893,047 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624777675,215 - 893,125 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSPPAT00000063778   ⟹   ENSPPAP00000040857
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
PanPan1.1 Ensembl4124,036,911 - 124,252,024 (-)Ensembl
RefSeq Acc Id: ENSPPAT00000063785   ⟹   ENSPPAP00000040864
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
PanPan1.1 Ensembl4124,040,103 - 124,252,928 (-)Ensembl
RefSeq Acc Id: ENSPPAT00000063789   ⟹   ENSPPAP00000040868
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
PanPan1.1 Ensembl4124,040,103 - 124,168,670 (-)Ensembl
RefSeq Acc Id: ENSPPAT00000063790   ⟹   ENSPPAP00000040869
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
PanPan1.1 Ensembl4124,055,322 - 124,252,060 (-)Ensembl
RefSeq Acc Id: ENSPPAT00000063792   ⟹   ENSPPAP00000040871
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
PanPan1.1 Ensembl4124,055,365 - 124,252,060 (-)Ensembl
RefSeq Acc Id: XM_034959083   ⟹   XP_034814974
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v23118,476,696 - 118,707,347 (-)NCBI
NHGRI_mPanPan14118,761,096 - 118,995,386 (-)NCBI
Mhudiblu_PPA_v04112,896,606 - 113,127,394 (-)NCBI
RefSeq Acc Id: XM_034959084   ⟹   XP_034814975
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v23118,476,696 - 118,707,343 (-)NCBI
NHGRI_mPanPan14118,761,096 - 118,995,386 (-)NCBI
Mhudiblu_PPA_v04112,896,606 - 113,127,387 (-)NCBI
RefSeq Acc Id: XM_063603885   ⟹   XP_063459955
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v23118,495,128 - 118,707,355 (-)NCBI
RefSeq Acc Id: XM_063603886   ⟹   XP_063459956
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v23118,542,518 - 118,707,353 (-)NCBI
RefSeq Acc Id: XM_063603887   ⟹   XP_063459957
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v23118,495,128 - 118,707,350 (-)NCBI
RefSeq Acc Id: XR_010112017
Type: NON-CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v23118,495,128 - 118,707,353 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_034814974   ⟸   XM_034959083
- Peptide Label: isoform X1
- UniProtKB: A0A2R9CQA7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_034814975   ⟸   XM_034959084
- Peptide Label: isoform X2
- UniProtKB: A0A2R9CQA7 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSPPAP00000040871   ⟸   ENSPPAT00000063792
RefSeq Acc Id: ENSPPAP00000040869   ⟸   ENSPPAT00000063790
RefSeq Acc Id: ENSPPAP00000040868   ⟸   ENSPPAT00000063789
RefSeq Acc Id: ENSPPAP00000040864   ⟸   ENSPPAT00000063785
RefSeq Acc Id: ENSPPAP00000040857   ⟸   ENSPPAT00000063778
RefSeq Acc Id: XP_063459955   ⟸   XM_063603885
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063459957   ⟸   XM_063603887
- Peptide Label: isoform X5
RefSeq Acc Id: XP_063459956   ⟸   XM_063603886
- Peptide Label: isoform X4
Protein Domains
C2H2-type   SET


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSPPAG00000043045 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSPPAT00000063778.1 UniProtKB/TrEMBL
  ENSPPAT00000063785.1 UniProtKB/TrEMBL
  ENSPPAT00000063789.1 UniProtKB/TrEMBL
  ENSPPAT00000063790.1 UniProtKB/TrEMBL
  ENSPPAT00000063792.1 UniProtKB/TrEMBL
Gene3D-CATH 2.170.270.10 UniProtKB/TrEMBL
  Classic Zinc Finger UniProtKB/TrEMBL
InterPro SET_dom UniProtKB/TrEMBL
  SET_dom_sf UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/TrEMBL
  Znf_C2H2_type UniProtKB/TrEMBL
  Znf_PRDM5-like UniProtKB/TrEMBL
NCBI Gene PRDM5 ENTREZGENE
PANTHER BLOODY FINGERS-RELATED UniProtKB/TrEMBL
  FI03704P-RELATED UniProtKB/TrEMBL
  GENE 10130-RELATED UniProtKB/TrEMBL
  IP01201P-RELATED UniProtKB/TrEMBL
  KRAB AND ZINC FINGER DOMAIN-CONTAINING UniProtKB/TrEMBL
  ZINC FINGER PROTEIN UniProtKB/TrEMBL
  ZINC FINGER PROTEIN UniProtKB/TrEMBL
  ZNF44 PROTEIN UniProtKB/TrEMBL
Pfam PRDM2_PR UniProtKB/TrEMBL
  zf-C2H2 UniProtKB/TrEMBL
  zf-C2H2_6 UniProtKB/TrEMBL
  zf-met UniProtKB/TrEMBL
PIRSF PRDM UniProtKB/TrEMBL
PROSITE SET UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_1 UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/TrEMBL
SMART ZnF_C2H2 UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/TrEMBL
UniProt A0A2R9CFX4_PANPA UniProtKB/TrEMBL
  A0A2R9CG27_PANPA UniProtKB/TrEMBL
  A0A2R9CG32_PANPA UniProtKB/TrEMBL
  A0A2R9CIK2_PANPA UniProtKB/TrEMBL
  A0A2R9CQA7 ENTREZGENE, UniProtKB/TrEMBL