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PRDM15 PR/SET domain 15 [ Homo sapiens (human) ]

Gene ID: 63977, updated on 23-Nov-2021

Summary

Official Symbol
PRDM15provided by HGNC
Official Full Name
PR/SET domain 15provided by HGNC
Primary source
HGNC:HGNC:13999
See related
Ensembl:ENSG00000141956 MIM:617692
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PFM15; ZNF298; C21orf83
Expression
Ubiquitous expression in lymph node (RPKM 2.4), appendix (RPKM 1.2) and 25 other tissues See more
Orthologs
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Genomic context

See PRDM15 in Genome Data Viewer
Location:
21q22.3
Exon count:
37
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 21 NC_000021.9 (41798225..41879396, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (43218385..43299453, complement)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 8078 Neighboring gene receptor interacting serine/threonine kinase 4 Neighboring gene uncharacterized LOC102724800 Neighboring gene Sharpr-MPRA regulatory region 172 Neighboring gene C2 calcium dependent domain containing 2 Neighboring gene small nucleolar RNA, H/ACA box 91 Neighboring gene zinc finger and BTB domain containing 21 Neighboring gene ZNF295 antisense RNA 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Genetic association with overall survival of taxane-treated lung cancer patients - A genome-wide association study in human lymphoblastoid cell lines followed by a clinical association study.
GeneReviews: Not available
Genome-wide association study of tanning phenotype in a population of European ancestry.
GeneReviews: Not available
Meta-analysis of Parkinson's disease: identification of a novel locus, RIT2.
GeneReviews: Not available

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • AP001619.2

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific 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 ISS
Inferred from Sequence or Structural Similarity
more info
 
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 ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
involved_in methylation IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of MAPK cascade ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of canonical Wnt signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of stem cell division ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
located_in nuclear body IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
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 

General protein information

Preferred Names
PR domain zinc finger protein 15
Names
PR domain 15
PR domain containing 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)

  1. NM_001040424.3NP_001035514.2  PR domain zinc finger protein 15 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks seven alternate in-frame exons and differs in the 3' UTR, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AB051812, AP002955, HY066601
    Consensus CDS
    CCDS42932.1
    Related
    ENSP00000381556.2, ENST00000398548.6
    Conserved Domains (6) summary
    COG5048
    Location:363825
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:692712
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:628649
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam16031
    Location:227310
    TonB_N; TonB N-terminal region
    pfam18445
    Location:1237
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19199
    Location:41166
    PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins
  2. NM_001282934.2NP_001269863.2  PR domain zinc finger protein 15 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks seven alternate in-frame exons, contains an alternate in-frame exon, and differs in the 3' UTR, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AP001619, AP002955, BC032305, HY066601
    Consensus CDS
    CCDS63370.1
    Related
    ENSP00000408592.2, ENST00000422911.6
    Conserved Domains (7) summary
    COG5048
    Location:676845
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:712732
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:648669
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:372394
    zf-C2H2; Zinc finger, C2H2 type
    pfam16031
    Location:227310
    TonB_N; TonB N-terminal region
    pfam18445
    Location:1237
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19199
    Location:41166
    PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins
  3. NM_022115.7NP_071398.5  PR domain zinc finger protein 15 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AB126081, AP001618, AP001619, AP002955
    Consensus CDS
    CCDS13676.1
    Related
    ENSP00000269844.4, ENST00000269844.5
    Conserved Domains (6) summary
    COG5048
    Location:429891
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:758778
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:694715
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18445
    Location:1237
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19199
    Location:107232
    PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins
    NF033909
    Location:293400
    opacity_OapA; opacity-associated protein OapA

RNA

  1. NR_104257.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) contains multiple differences in the internal exons and differs in the 3' terminal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB051814, AB126081, AP002955
    Related
    ENST00000449395.6
  2. NR_104258.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) contains multiple differences in the internal exons and differs in the 3' terminal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB051815, AB126081, AP002955
    Related
    ENST00000441787.5
  3. NR_104260.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) contains multiple differences, including use of an alternate 3' exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB126081, AP001618, AP002955, AY063456, BC067102
  4. NR_135464.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) contains multiple differences, including use of an alternate 3' exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF276513, AP002955, AY063456, BM544857, BM755202, CA949877, CF135664, CF137278, CF138151, CN400247, EC485279, HY003319, HY146343

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p13 Primary Assembly

    Range
    41798225..41879396 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011529674.1XP_011527976.1  PR domain zinc finger protein 15 isoform X2

    Conserved Domains (7) summary
    smart00317
    Location:86202
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    COG5048
    Location:366819
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:715735
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:651672
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:375397
    zf-C2H2; Zinc finger, C2H2 type
    pfam06217
    Location:213283
    GAGA_bind; GAGA binding protein-like family
    pfam13465
    Location:727752
    zf-H2C2_2; Zinc-finger double domain
  2. XM_006724040.2XP_006724103.1  PR domain zinc finger protein 15 isoform X6

    Conserved Domains (7) summary
    smart00317
    Location:86202
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    COG5048
    Location:400818
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:685705
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:621642
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:409431
    zf-C2H2; Zinc finger, C2H2 type
    pfam06217
    Location:252317
    GAGA_bind; GAGA binding protein-like family
    pfam13465
    Location:697722
    zf-H2C2_2; Zinc-finger double domain
  3. XM_006724039.2XP_006724102.1  PR domain zinc finger protein 15 isoform X4

    Conserved Domains (7) summary
    smart00317
    Location:86202
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    COG5048
    Location:400838
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:705725
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:641662
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:409431
    zf-C2H2; Zinc finger, C2H2 type
    pfam06217
    Location:252317
    GAGA_bind; GAGA binding protein-like family
    pfam13465
    Location:717742
    zf-H2C2_2; Zinc-finger double domain
  4. XM_011529683.1XP_011527985.1  PR domain zinc finger protein 15 isoform X7

    Conserved Domains (7) summary
    smart00317
    Location:349465
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    COG5048
    Location:6631125
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:9921012
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:928949
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:672694
    zf-C2H2; Zinc finger, C2H2 type
    pfam06217
    Location:515580
    GAGA_bind; GAGA binding protein-like family
    pfam13465
    Location:10041029
    zf-H2C2_2; Zinc-finger double domain
  5. XM_011529675.1XP_011527977.1  PR domain zinc finger protein 15 isoform X3

    See identical proteins and their annotated locations for XP_011527977.1

    Conserved Domains (7) summary
    COG5048
    Location:676845
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:712732
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:648669
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:372394
    zf-C2H2; Zinc finger, C2H2 type
    pfam16031
    Location:227310
    TonB_N; TonB N-terminal region
    pfam18445
    Location:1237
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19199
    Location:41166
    PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins
  6. XM_017028425.1XP_016883914.1  PR domain zinc finger protein 15 isoform X5

    UniProtKB/TrEMBL
    E7ER26
    Related
    ENSP00000431410.1, ENST00000447016.6
    Conserved Domains (6) summary
    COG5048
    Location:363825
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:692712
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:628649
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam16031
    Location:227310
    TonB_N; TonB N-terminal region
    pfam18445
    Location:1237
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19199
    Location:41166
    PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins
  7. XM_011529678.2XP_011527980.1  PR domain zinc finger protein 15 isoform X3

    See identical proteins and their annotated locations for XP_011527980.1

    Conserved Domains (7) summary
    COG5048
    Location:676845
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:712732
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:648669
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:372394
    zf-C2H2; Zinc finger, C2H2 type
    pfam16031
    Location:227310
    TonB_N; TonB N-terminal region
    pfam18445
    Location:1237
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19199
    Location:41166
    PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins
  8. XM_011529681.3XP_011527983.1  PR domain zinc finger protein 15 isoform X1

    See identical proteins and their annotated locations for XP_011527983.1

    Conserved Domains (7) summary
    smart00317
    Location:53169
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    COG5048
    Location:367820
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:716736
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:652673
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:376398
    zf-C2H2; Zinc finger, C2H2 type
    pfam06217
    Location:219284
    GAGA_bind; GAGA binding protein-like family
    pfam13465
    Location:728753
    zf-H2C2_2; Zinc-finger double domain
  9. XM_011529676.2XP_011527978.1  PR domain zinc finger protein 15 isoform X3

    See identical proteins and their annotated locations for XP_011527978.1

    Conserved Domains (7) summary
    COG5048
    Location:676845
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:712732
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:648669
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:372394
    zf-C2H2; Zinc finger, C2H2 type
    pfam16031
    Location:227310
    TonB_N; TonB N-terminal region
    pfam18445
    Location:1237
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19199
    Location:41166
    PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins
  10. XM_017028426.1XP_016883915.1  PR domain zinc finger protein 15 isoform X5

    UniProtKB/TrEMBL
    E7ER26
    Conserved Domains (6) summary
    COG5048
    Location:363825
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:692712
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:628649
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam16031
    Location:227310
    TonB_N; TonB N-terminal region
    pfam18445
    Location:1237
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19199
    Location:41166
    PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins
  11. XM_011529677.2XP_011527979.1  PR domain zinc finger protein 15 isoform X3

    See identical proteins and their annotated locations for XP_011527979.1

    Conserved Domains (7) summary
    COG5048
    Location:676845
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:712732
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:648669
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:372394
    zf-C2H2; Zinc finger, C2H2 type
    pfam16031
    Location:227310
    TonB_N; TonB N-terminal region
    pfam18445
    Location:1237
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19199
    Location:41166
    PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins
  12. XM_011529679.2XP_011527981.1  PR domain zinc finger protein 15 isoform X3

    See identical proteins and their annotated locations for XP_011527981.1

    Conserved Domains (7) summary
    COG5048
    Location:676845
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:712732
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:648669
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:372394
    zf-C2H2; Zinc finger, C2H2 type
    pfam16031
    Location:227310
    TonB_N; TonB N-terminal region
    pfam18445
    Location:1237
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19199
    Location:41166
    PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins

RNA

  1. XR_001754887.1 RNA Sequence

  2. XR_001754886.1 RNA Sequence

  3. XR_937542.1 RNA Sequence

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