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ZIM2 zinc finger imprinted 2 [ Homo sapiens (human) ]

Gene ID: 23619, updated on 27-Nov-2024

Summary

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Official Symbol
ZIM2provided by HGNC
Official Full Name
zinc finger imprinted 2provided by HGNC
Primary source
HGNC:HGNC:12875
See related
Ensembl:ENSG00000269699 AllianceGenome:HGNC:12875
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ZNF656
Summary
In human, ZIM2 and PEG3 (GeneID:5178) are two distinct genes that share a set of 5' exons and have a common promoter, and both genes are paternally expressed. Alternative splicing events connect the shared exons either with the remaining 4 exons unique to ZIM2, or with the remaining 2 exons unique to PEG3. This is in contrast to mouse and cow, where ZIM2 and PEG3 genes do not share exons in common, and the imprinting status of ZIM2 is also not conserved amongst mammals. Additional 5' alternatively spliced transcripts encoding the same protein have been found for the human ZIM2 gene. [provided by RefSeq, Oct 2010]
Expression
Biased expression in ovary (RPKM 34.2), placenta (RPKM 19.3) and 4 other tissues See more
Orthologs
all
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Genomic context

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See ZIM2 in Genome Data Viewer
Location:
19q13.43
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (56774547..56840726, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (59869633..59935794, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (57285915..57352094, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372473 Neighboring gene uncharacterized LOC105372472 Neighboring gene olfactory receptor family 5 subfamily AH member 1 pseudogene Neighboring gene ZIM2 antisense RNA 1 Neighboring gene PEG3 antisense RNA 1 Neighboring gene paternally expressed 3 Neighboring gene MER1 repeat containing imprinted transcript 1 Neighboring gene uncharacterized LOC124904779

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Exon sharing of a novel human zinc-finger gene, ZIM2, and paternally expressed gene 3 (PEG3). Kim J, et al. Genomics, 2000 Feb 15. PMID 10708526
  2. Lineage-specific imprinting and evolution of the zinc-finger gene ZIM2. Kim J, et al. Genomics, 2004 Jul. PMID 15203203
  3. A GO catalogue of human DNA-binding transcription factors. Lovering RC, et al. Biochim Biophys Acta Gene Regul Mech, 2021 Nov-Dec. PMID 34673265
  4. Identification of proteins that interact with alpha A-crystallin using a human proteome microarray. Fan Q, et al. Mol Vis, 2014. PMID 24453475, Free PMC Article
  5. The HIV-1 Tat protein recruits a ubiquitin ligase to reorganize the 7SK snRNP for transcriptional activation. Faust TB, et al. Elife, 2018 May 30. PMID 29845934, Free PMC Article

See all (11) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Copy number response

Description
Copy number response
Haploinsufficency

No evidence available (Last evaluated 2012-05-17)

ClinGen Genome Curation Page
Triplosensitivity

No evidence available (Last evaluated 2012-05-17)

ClinGen Genome Curation Page

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity NAS
Non-traceable Author Statement
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables zinc ion binding NAS
Non-traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in regulation of DNA-templated transcription NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
zinc finger imprinted 2
Names
zinc finger protein 656

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.

Genomic

  1. NG_012989.1 RefSeqGene

    Range
    5004..71183
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001146326.2 → NP_001139798.1  zinc finger imprinted 2 isoform b

    See identical proteins and their annotated locations for NP_001139798.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an additional 5' non-coding exon, therefore, differs in the 5' UTR compared to variant 1. Variants 1-6, 14, and 15 all encode the same isoform (b).
    Source sequence(s)
    AF166122, AI418432, BC104876, DC400394
    Consensus CDS
    CCDS33123.1
    UniProtKB/Swiss-Prot
    Q2M3K1, Q9NZV7
    Related
    ENSP00000470326.1, ENST00000601070.5
    Conserved Domains (4) summary
    smart00349
    Location:176 → 232
    KRAB; krueppel associated box
    sd00017
    Location:414 → 434
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:466 → 488
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:342 → 365
    zf-H2C2_2; Zinc-finger double domain

  2. NM_001146327.2 → NP_001139799.1  zinc finger imprinted 2 isoform b

    See identical proteins and their annotated locations for NP_001139799.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an additional 5' non-coding exon and uses a different acceptor splice site at one of the 5' non-coding exons, therefore, differs in the 5' UTR compared to variant 1. Variants 1-6, 14, and 15 all encode the same isoform (b).
    Source sequence(s)
    AF166122, AI418432, BC104878, DC400394
    Consensus CDS
    CCDS33123.1
    UniProtKB/Swiss-Prot
    Q2M3K1, Q9NZV7
    Conserved Domains (4) summary
    smart00349
    Location:176 → 232
    KRAB; krueppel associated box
    sd00017
    Location:414 → 434
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:466 → 488
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:342 → 365
    zf-H2C2_2; Zinc-finger double domain

  3. NM_001369770.1 → NP_001356699.1  zinc finger imprinted 2 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4), as well as variants 1-3, 5, 6, 14, and 15, encodes isoform b.
    Source sequence(s)
    AC006115
    Consensus CDS
    CCDS33123.1
    UniProtKB/Swiss-Prot
    Q2M3K1, Q9NZV7
    Related
    ENSP00000468984.1, ENST00000599935.5
    Conserved Domains (4) summary
    smart00349
    Location:176 → 232
    KRAB; krueppel associated box
    sd00017
    Location:414 → 434
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:466 → 488
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:342 → 365
    zf-H2C2_2; Zinc-finger double domain

  4. NM_001369771.1 → NP_001356700.1  zinc finger imprinted 2 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5), as well as variants 1-4, 6, 14, and 15, encodes isoform b.
    Source sequence(s)
    AC006115
    Consensus CDS
    CCDS33123.1
    UniProtKB/Swiss-Prot
    Q2M3K1, Q9NZV7
    Conserved Domains (4) summary
    smart00349
    Location:176 → 232
    KRAB; krueppel associated box
    sd00017
    Location:414 → 434
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:466 → 488
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:342 → 365
    zf-H2C2_2; Zinc-finger double domain

  5. NM_001369772.1 → NP_001356701.1  zinc finger imprinted 2 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6), as well as variants 1-5, 14, and 15, encodes isoform b.
    Source sequence(s)
    AC006115
    Consensus CDS
    CCDS33123.1
    UniProtKB/Swiss-Prot
    Q2M3K1, Q9NZV7
    Related
    ENSP00000472306.1, ENST00000593711.6
    Conserved Domains (4) summary
    smart00349
    Location:176 → 232
    KRAB; krueppel associated box
    sd00017
    Location:414 → 434
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:466 → 488
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:342 → 365
    zf-H2C2_2; Zinc-finger double domain

  6. NM_001369773.1 → NP_001356702.1  zinc finger imprinted 2 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7), as well as variants 8 and 13, encodes the longer isoform (a).
    Source sequence(s)
    AC006115
    Consensus CDS
    CCDS92697.1
    UniProtKB/TrEMBL
    A0A8I5KWX0
    Related
    ENSP00000510784.1, ENST00000689654.1
    Conserved Domains (4) summary
    smart00349
    Location:207 → 263
    KRAB; krueppel associated box
    sd00017
    Location:445 → 465
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:497 → 519
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:373 → 396
    zf-H2C2_2; Zinc-finger double domain

  7. NM_001369774.1 → NP_001356703.1  zinc finger imprinted 2 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8), as well as variants 7 and 13, encodes the longer isoform (a).
    Source sequence(s)
    AC006115
    Consensus CDS
    CCDS92697.1
    UniProtKB/TrEMBL
    A0A8I5KWX0
    Conserved Domains (4) summary
    smart00349
    Location:207 → 263
    KRAB; krueppel associated box
    sd00017
    Location:445 → 465
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:497 → 519
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:373 → 396
    zf-H2C2_2; Zinc-finger double domain

  8. NM_001387356.1 → NP_001374285.1  zinc finger imprinted 2 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (13), as well as variants 7 and 8, encodes the longer isoform (a).
    Source sequence(s)
    AC006115
    Consensus CDS
    CCDS92697.1
    UniProtKB/TrEMBL
    A0A8I5KWX0
    Related
    ENSP00000486502.2, ENST00000629319.3
    Conserved Domains (4) summary
    smart00349
    Location:207 → 263
    KRAB; krueppel associated box
    sd00017
    Location:445 → 465
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:497 → 519
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:373 → 396
    zf-H2C2_2; Zinc-finger double domain

  9. NM_001387357.1 → NP_001374286.1  zinc finger imprinted 2 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (14), as well as variants 1-6 and 15, encodes isoform b.
    Source sequence(s)
    AC006115
    Consensus CDS
    CCDS33123.1
    UniProtKB/Swiss-Prot
    Q2M3K1, Q9NZV7
    Conserved Domains (4) summary
    smart00349
    Location:176 → 232
    KRAB; krueppel associated box
    sd00017
    Location:414 → 434
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:466 → 488
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:342 → 365
    zf-H2C2_2; Zinc-finger double domain

  10. NM_001387358.1 → NP_001374287.1  zinc finger imprinted 2 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (15), as well as variants 1-6 and 14, encodes isoform b.
    Source sequence(s)
    AC006115
    Consensus CDS
    CCDS33123.1
    UniProtKB/Swiss-Prot
    Q2M3K1, Q9NZV7
    Conserved Domains (4) summary
    smart00349
    Location:176 → 232
    KRAB; krueppel associated box
    sd00017
    Location:414 → 434
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:466 → 488
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:342 → 365
    zf-H2C2_2; Zinc-finger double domain

  11. NM_015363.5 → NP_056178.3  zinc finger imprinted 2 isoform b

    See identical proteins and their annotated locations for NP_056178.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) was originally described as the ZIM2 transcript (PMID:10708526). Variants 1-6, 14, and 15 all encode the same isoform (b).
    Source sequence(s)
    AF166122, AI418432, DC400394
    Consensus CDS
    CCDS33123.1
    UniProtKB/Swiss-Prot
    Q2M3K1, Q9NZV7
    Conserved Domains (4) summary
    smart00349
    Location:176 → 232
    KRAB; krueppel associated box
    sd00017
    Location:414 → 434
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:466 → 488
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:342 → 365
    zf-H2C2_2; Zinc-finger double domain

RNA

  1. NR_163140.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC006115
    Related
    ENST00000693159.1

  2. NR_163141.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC006115
    Related
    ENST00000595671.5

  3. NR_163142.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC006115

  4. NR_163143.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC006115
    Related
    ENST00000650111.1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    56774547..56840726 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    59869633..59935794 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NZV7.1 GenPept UniProtKB/Swiss-Prot:Q9NZV7

Gene LinkOut

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