Prdm5 (PR/SET domain 5) - Rat Genome Database

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Gene: Prdm5 (PR/SET domain 5) Chinchilla lanigera
Analyze
Symbol: Prdm5
Name: PR/SET domain 5
RGD ID: 8769859
Description: ENCODES a protein that exhibits DNA-binding transcription factor binding (ortholog); DNA-binding transcription repressor activity, RNA polymerase II-specific (ortholog); RNA polymerase II cis-regulatory region sequence-specific DNA binding (ortholog); INVOLVED IN cellular response to leukemia inhibitory factor (ortholog); mitotic cell cycle (ortholog); negative regulation of DNA-templated transcription (ortholog); ASSOCIATED WITH Axenfeld-Rieger syndrome type 1 (ortholog); brittle cornea syndrome 1 (ortholog); brittle cornea syndrome 2 (ortholog); FOUND IN nuclear body (ortholog); nucleolus (ortholog); nucleoplasm (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: PR domain containing 5; PR domain zinc finger protein 5
RGD Orthologs
Human
Mouse
Rat
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: ChiLan1.0 - Chinchilla ChiLan1.0 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

References - curated
# Reference Title Reference Citation
1. Transitive Annotation Pipeline Automated assignment of GO, PW and RDO ISO annotations across species
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
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
(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
(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
(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: ENSCLAT00000007806   ⟹   ENSCLAP00000007687
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_00495542819,714,730 - 19,881,917 (+)Ensembl
RefSeq Acc Id: ENSCLAT00000007807   ⟹   ENSCLAP00000007688
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_00495542819,714,897 - 19,878,606 (+)Ensembl
RefSeq Acc Id: ENSCLAT00000007808   ⟹   ENSCLAP00000007689
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_00495542819,714,897 - 19,871,872 (+)Ensembl
RefSeq Acc Id: ENSCLAT00000007809   ⟹   ENSCLAP00000007690
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_00495542819,750,273 - 19,878,606 (+)Ensembl
RefSeq Acc Id: XM_013515254   ⟹   XP_013370708
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_00495542819,684,721 - 19,881,716 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_013370708 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCLAP00000007687
  ENSCLAP00000007687.1
  ENSCLAP00000007688.1
  ENSCLAP00000007689.1
  ENSCLAP00000007690.1
Reference Protein Sequences
RefSeq Acc Id: XP_013370708   ⟸   XM_013515254
- UniProtKB: A0A8C2V3P1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCLAP00000007687   ⟸   ENSCLAT00000007806
RefSeq Acc Id: ENSCLAP00000007688   ⟸   ENSCLAT00000007807
RefSeq Acc Id: ENSCLAP00000007689   ⟸   ENSCLAT00000007808
RefSeq Acc Id: ENSCLAP00000007690   ⟸   ENSCLAT00000007809
Protein Domains
C2H2-type   SET


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCLAG00000005392 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCLAT00000007806 ENTREZGENE
  ENSCLAT00000007806.1 UniProtKB/TrEMBL
  ENSCLAT00000007807.1 UniProtKB/TrEMBL
  ENSCLAT00000007808.1 UniProtKB/TrEMBL
  ENSCLAT00000007809.1 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 FEZ FAMILY ZINC FINGER PROTEIN ERM UniProtKB/TrEMBL
  IP01201P-RELATED UniProtKB/TrEMBL
  KRUEPPEL-LIKE FACTOR 15 UniProtKB/TrEMBL
  KRUEPPEL-LIKE TRANSCRIPTION FACTOR UniProtKB/TrEMBL
  PR DOMAIN ZINC FINGER PROTEIN 5 UniProtKB/TrEMBL
  ZINC FINGER AND SCAN DOMAIN-CONTAINING UniProtKB/TrEMBL
  ZINC FINGER 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 A0A8C2UYL8_CHILA UniProtKB/TrEMBL
  A0A8C2UYM5_CHILA UniProtKB/TrEMBL
  A0A8C2UZ93_CHILA UniProtKB/TrEMBL
  A0A8C2V3P1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-08-03 Prdm5  PR/SET domain 5    PR domain containing 5  Symbol and/or name change 5135510 APPROVED