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

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Gene: PRDM5 (PR/SET domain 5) Chlorocebus sabaeus
Analyze
Symbol: PRDM5
Name: PR/SET domain 5
RGD ID: 18441476
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 zinc finger protein 5
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: ChlSab1.1 - Green Monkey 1.1 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
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
(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
(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
(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


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

endocrine system hemolymphoid system nervous system
High
Medium 14 14
Low 22 10 46
Below cutoff 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSCSAT00000001758   ⟹   ENSCSAP00000000098
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1 Ensembl767,987,359 - 68,206,893 (-)Ensembl
RefSeq Acc Id: XM_007999676   ⟹   XP_007997867
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1767,985,784 - 68,207,113 (-)NCBI
Vero_WHO_p1.0NW_02366603746,952,855 - 47,174,018 (-)NCBI
Sequence:
RefSeq Acc Id: XM_007999677   ⟹   XP_007997868
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1767,985,387 - 68,207,113 (-)NCBI
Vero_WHO_p1.0NW_02366603746,953,805 - 47,174,018 (-)NCBI
Sequence:
RefSeq Acc Id: XM_037991424   ⟹   XP_037847352
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366603746,952,855 - 47,174,019 (-)NCBI
RefSeq Acc Id: XM_037991433   ⟹   XP_037847361
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366603746,971,323 - 47,174,018 (-)NCBI
RefSeq Acc Id: XR_005238255
Type: NON-CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366603747,009,542 - 47,174,018 (-)NCBI
RefSeq Acc Id: XR_005238256
Type: NON-CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366603747,012,927 - 47,174,018 (-)NCBI
Protein Sequences
Protein RefSeqs XP_007997867 (Get FASTA)   NCBI Sequence Viewer  
  XP_007997868 (Get FASTA)   NCBI Sequence Viewer  
  XP_037847352 (Get FASTA)   NCBI Sequence Viewer  
  XP_037847361 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCSAP00000000098
  ENSCSAP00000000098.1
Reference Protein Sequences
RefSeq Acc Id: XP_007997868   ⟸   XM_007999677
- Peptide Label: isoform X2
- UniProtKB: A0A0D9QUQ9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_007997867   ⟸   XM_007999676
- Peptide Label: isoform X1
RefSeq Acc Id: ENSCSAP00000000098   ⟸   ENSCSAT00000001758
RefSeq Acc Id: XP_037847352   ⟸   XM_037991424
- Peptide Label: isoform X3
RefSeq Acc Id: XP_037847361   ⟸   XM_037991433
- Peptide Label: isoform X4


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCSAG00000003729 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCSAT00000001758.1 UniProtKB/TrEMBL
Gene3D-CATH 2.170.270.10 UniProtKB/TrEMBL
  Classic Zinc Finger UniProtKB/TrEMBL
InterPro PRDM5_PR-SET UniProtKB/TrEMBL
  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 GENE 10130-RELATED UniProtKB/TrEMBL
  ZNF44 PROTEIN UniProtKB/TrEMBL
Pfam PRDM2_PR UniProtKB/TrEMBL
  zf-C2H2 UniProtKB/TrEMBL
  zf-C2H2_6 UniProtKB/TrEMBL
PIRSF PRDM UniProtKB/TrEMBL
PROSITE SET UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_1 UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/TrEMBL
SMART SET UniProtKB/TrEMBL
  ZnF_C2H2 UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/TrEMBL
  SSF82199 UniProtKB/TrEMBL
UniProt A0A0D9QUQ9 ENTREZGENE, UniProtKB/TrEMBL