Prdm15 PR domain containing 15 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Prdm15provided by MGI
Official Full Name: PR domain containing 15provided by MGI
Primary source: MGI:MGI:1930121
See related: Ensembl:ENSMUSG00000014039 AllianceGenome:MGI:1930121
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: ORF62; Zfp298; C21orf83; E130018M06Rik
Summary: Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and promoter-specific chromatin binding activity. Involved in positive regulation of transcription by RNA polymerase II; regulation of signal transduction; and regulation of stem cell division. Located in nucleus. Is expressed in several structures, including central nervous system; genitourinary system; incisor; sensory organ; and skin. Orthologous to human PRDM15 (PR/SET domain 15). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in thymus adult (RPKM 6.0), whole brain E14.5 (RPKM 4.9) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 16; 16 C4

Exon count:: 26

Annotation release	Status	Assembly	Chr	Location
109	current	GRCm39 (GCF_000001635.27)	16	NC_000082.7 (97592667..97653076, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	16	NC_000082.6 (97791467..97851875, complement)

Chromosome 16 - NC_000082.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PRDM15 loss of function links NOTCH and WNT/PCP signaling to patterning defects in holoprosencephaly.
Title: PRDM15 loss of function links NOTCH and WNT/PCP signaling to patterning defects in holoprosencephaly.
Findings indicate that PR domain containing 15 protein (PRDM15) is important in both mouse and human induced pluripotent stem cells (iPSCs) reprogramming.
Title: PRDM15 safeguards naive pluripotency by transcriptionally regulating WNT and MAPK-ERK signaling.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (3) 1 citation
Endonuclease-mediated (3)

General gene information

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Markers

UniSTS:259130 (e-PCR)
- UniSTS:259130

Prdm15 (e-PCR), detects polymorphism
- UniSTS:259130

Prdm15 (e-PCR), detects polymorphism
- UniSTS:259131

G67860 (e-PCR)
- UniSTS:228508

D16Mit106 (e-PCR), detects polymorphism
- UniSTS:127733

Homology

Homologs of the Prdm15 gene: The Prdm15 gene is conserved in human, chimpanzee, Rhesus monkey, dog, cow, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 491 organisms have orthologs with human gene Prdm15
Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables promoter-specific chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables transferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cell fate commitment	IBA Inferred from Biological aspect of Ancestor more info	PubMed
acts_upstream_of_or_within methylation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within multicellular organism development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of MAPK cascade	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of canonical Wnt signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of stem cell division	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in nuclear body	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: PR domain zinc finger protein 15

Names: PR domain-containing protein 15; zinc finger protein 298

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001359077.2 → NP_001346006.1 PR domain zinc finger protein 15 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) contains a distinct 5' UTR and lacks an in-frame portion of the 5' coding region, compared to variant 1. The resulting isoform (2) has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AC121560

Consensus CDS

CCDS88979.1

Related

ENSMUSP00000113791.2, ENSMUST00000121584.8

Conserved Domains (4) summary

COG5048
Location:665 → 834

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:701 → 721

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam18445
Location:12 → 37

zf_PR_Knuckle; PR zinc knuckle motif

cd19199
Location:41 → 166

PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins
NM_001359078.2 → NP_001346007.1 PR domain zinc finger protein 15 isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) has multiple differences, compared to variant 1. These differences result in a distinct 5' UTR and cause translation initiation at a downstream start codon, compared to variant 1. The encoded protein (isoform 3) is shorter than isoform 1.

Source sequence(s)

AC121560

Conserved Domains (2) summary

COG5048
Location:162 → 331

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:198 → 218

ZF_C2H2; C2H2 Zn finger [structural motif]
NM_001403426.1 → NP_001390355.1 PR domain zinc finger protein 15 isoform 2

Status: VALIDATED

Source sequence(s)

AC121560
NM_001403427.1 → NP_001390356.1 PR domain zinc finger protein 15 isoform 4

Status: VALIDATED

Source sequence(s)

AC121560
NM_001403428.1 → NP_001390357.1 PR domain zinc finger protein 15 isoform 4

Status: VALIDATED

Source sequence(s)

AC121560
NM_001403429.1 → NP_001390358.1 PR domain zinc finger protein 15 isoform 5

Status: VALIDATED

Source sequence(s)

AC121560
NM_001403430.1 → NP_001390359.1 PR domain zinc finger protein 15 isoform 6

Status: VALIDATED

Source sequence(s)

AC121560
NM_001403431.1 → NP_001390360.1 PR domain zinc finger protein 15 isoform 7

Status: VALIDATED

Source sequence(s)

AC121560
NM_001403432.1 → NP_001390361.1 PR domain zinc finger protein 15 isoform 8

Status: VALIDATED

Source sequence(s)

AC121560
NM_001403437.1 → NP_001390366.1 PR domain zinc finger protein 15 isoform 9

Status: VALIDATED

Source sequence(s)

AC121560
NM_001403438.1 → NP_001390367.1 PR domain zinc finger protein 15 isoform 10

Status: VALIDATED

Source sequence(s)

AC121560
NM_144789.2 → NP_659038.2 PR domain zinc finger protein 15 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AC121560

Consensus CDS

CCDS49926.1

UniProtKB/Swiss-Prot

Q3UML7

UniProtKB/TrEMBL

E9Q8T2

Related

ENSMUSP00000093533.4, ENSMUST00000095849.10

Conserved Domains (3) summary

COG5048
Location:691 → 860

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:727 → 747

ZF_C2H2; C2H2 Zn finger [structural motif]

cl02566
Location:76 → 191

SET; SET domain

RNA

NR_175376.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC121560
NR_175377.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC121560

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000082.7 Reference GRCm39 C57BL/6J

Range

97592667..97653076 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030248930.2 → XP_030104790.1 PR domain zinc finger protein 15 isoform X6

Conserved Domains (4) summary

COG5048
Location:662 → 831

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:698 → 718

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam18445
Location:48 → 73

zf_PR_Knuckle; PR zinc knuckle motif

cd19199
Location:77 → 202

PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins
XM_006522866.5 → XP_006522929.1 PR domain zinc finger protein 15 isoform X4

Conserved Domains (4) summary

COG5048
Location:667 → 836

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:703 → 723

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam18445
Location:48 → 73

zf_PR_Knuckle; PR zinc knuckle motif

cd19199
Location:77 → 202

PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins
XM_006522865.5 → XP_006522928.1 PR domain zinc finger protein 15 isoform X3

Conserved Domains (4) summary

COG5048
Location:667 → 836

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:703 → 723

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam18445
Location:48 → 73

zf_PR_Knuckle; PR zinc knuckle motif

cd19199
Location:77 → 202

PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins
XM_006522864.5 → XP_006522927.1 PR domain zinc finger protein 15 isoform X1

Conserved Domains (4) summary

COG5048
Location:696 → 865

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:732 → 752

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam18445
Location:48 → 73

zf_PR_Knuckle; PR zinc knuckle motif

cd19199
Location:77 → 202

PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins
XM_036159744.1 → XP_036015637.1 PR domain zinc finger protein 15 isoform X9

Conserved Domains (4) summary

COG5048
Location:626 → 795

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:662 → 682

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam18445
Location:12 → 37

zf_PR_Knuckle; PR zinc knuckle motif

cd19199
Location:41 → 166

PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins
XM_030248931.2 → XP_030104791.1 PR domain zinc finger protein 15 isoform X8

Conserved Domains (4) summary

COG5048
Location:631 → 800

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:667 → 687

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam18445
Location:12 → 37

zf_PR_Knuckle; PR zinc knuckle motif

cd19199
Location:41 → 166

PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins
XM_006522870.5 → XP_006522933.1 PR domain zinc finger protein 15 isoform X7

Conserved Domains (4) summary

COG5048
Location:660 → 829

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:696 → 716

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam18445
Location:12 → 37

zf_PR_Knuckle; PR zinc knuckle motif

cd19199
Location:41 → 166

PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins
XM_006522869.5 → XP_006522932.1 PR domain zinc finger protein 15 isoform X5

UniProtKB/TrEMBL

E9Q6A1

Conserved Domains (4) summary

COG5048
Location:665 → 834

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:701 → 721

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam18445
Location:12 → 37

zf_PR_Knuckle; PR zinc knuckle motif

cd19199
Location:41 → 166

PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins
XM_030248932.2 → XP_030104792.1 PR domain zinc finger protein 15 isoform X10

Conserved Domains (3) summary

COG5048
Location:549 → 718

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:585 → 605

ZF_C2H2; C2H2 Zn finger [structural motif]

cl40432
Location:1 → 50

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
XM_030248933.2 → XP_030104793.1 PR domain zinc finger protein 15 isoform X12

Conserved Domains (2) summary

COG5048
Location:193 → 362

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:229 → 249

ZF_C2H2; C2H2 Zn finger [structural motif]
XM_036159746.1 → XP_036015639.1 PR domain zinc finger protein 15 isoform X12

Conserved Domains (2) summary

COG5048
Location:193 → 362

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:229 → 249

ZF_C2H2; C2H2 Zn finger [structural motif]
XM_036159745.1 → XP_036015638.1 PR domain zinc finger protein 15 isoform X11

Conserved Domains (3) summary

COG5048
Location:510 → 679

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:546 → 566

ZF_C2H2; C2H2 Zn finger [structural motif]

cl40432
Location:1 → 50

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
XM_030248929.2 → XP_030104789.1 PR domain zinc finger protein 15 isoform X2

Conserved Domains (4) summary

COG5048
Location:394 → 855

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:722 → 742

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam18445
Location:38 → 63

zf_PR_Knuckle; PR zinc knuckle motif

cd19199
Location:67 → 192

PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins
XM_006522868.5 → XP_006522931.1 PR domain zinc finger protein 15 isoform X10

See identical proteins and their annotated locations for XP_006522931.1

Conserved Domains (3) summary

COG5048
Location:549 → 718

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:585 → 605

ZF_C2H2; C2H2 Zn finger [structural motif]

cl40432
Location:1 → 50

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily