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

    Gene ID: 23619, updated on 2-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 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)

    Genotypes

    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
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  
    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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