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    ANKRD42 ankyrin repeat domain 42 [ Homo sapiens (human) ]

    Gene ID: 338699, updated on 5-Mar-2024

    Summary

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    Official Symbol
    ANKRD42provided by HGNC
    Official Full Name
    ankyrin repeat domain 42provided by HGNC
    Primary source
    HGNC:HGNC:26752
    See related
    Ensembl:ENSG00000137494 MIM:619778; AllianceGenome:HGNC:26752
    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
    SARP; PPP1R79
    Summary
    Predicted to enable NF-kappaB binding activity. Predicted to act upstream of or within positive regulation of NF-kappaB transcription factor activity and positive regulation of cytokine production involved in inflammatory response. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in testis (RPKM 10.9), thyroid (RPKM 3.7) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ANKRD42 in Genome Data Viewer
    Location:
    11q14.1
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (83193712..83256099)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (83130185..83192552)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (82904754..82967141)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902726 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3819 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5347 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:82868143-82868932 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3820 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:82877478-82878677 Neighboring gene PCF11 cleavage and polyadenylation factor subunit Neighboring gene ANKRD42 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5349 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5350 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:82904985-82905163 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5351 Neighboring gene PCF11 antisense RNA 1 Neighboring gene CDC28 protein kinase regulatory subunit 1B pseudogene 4 Neighboring gene ribosomal protein L32 pseudogene 24 Neighboring gene Sharpr-MPRA regulatory region 3734 Neighboring gene coiled-coil domain containing 90B Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:82996183-82996779 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:82996780-82997375 Neighboring gene CCDC90B antisense RNA 1 Neighboring gene uncharacterized LOC105369420

    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. SARP, a new alternatively spliced protein phosphatase 1 and DNA interacting protein. Browne GJ, et al. Biochem J, 2007 Feb 15. PMID 17123353, Free PMC Article
    2. Identification of the human testis protein phosphatase 1 interactome. Fardilha M, et al. Biochem Pharmacol, 2011 Nov 15. PMID 21382349
    3. Systematic identification of cancer cell vulnerabilities to natural killer cell-mediated immune surveillance. Pech MF, et al. Elife, 2019 Aug 27. PMID 31452512, Free PMC Article
    4. Upregulation of RIN3 induces endosomal dysfunction in Alzheimer's disease. Shen R, et al. Transl Neurodegener, 2020 Jun 18. PMID 32552912, Free PMC Article
    5. An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations. Liu X, et al. Nat Commun, 2018 Mar 22. PMID 29568061, Free PMC Article

    See all (10) 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

    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

    Clone Names

    • FLJ37874

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables NF-kappaB binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in positive regulation of NF-kappaB transcription factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    ankyrin repeat domain-containing protein 42
    Names
    protein phosphatase 1, regulatory subunit 79
    several ankyrin repeat protein

    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_001300972.2 → NP_001287901.1  ankyrin repeat domain-containing protein 42 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AP000873, BC045621, BU674837, DQ508815
      Consensus CDS
      CCDS76458.1
      UniProtKB/TrEMBL
      A1XPJ0, E9PP91
      Related
      ENSP00000434666.1, ENST00000531895.5
      Conserved Domains (3) summary
      cd00204
      Location:59 → 179
      ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
      sd00045
      Location:59 → 90
      ANK; ANK repeat [structural motif]
      cl25732
      Location:332 → 482
      SMC_N; RecF/RecN/SMC N terminal domain

    2. NM_001300973.2 → NP_001287902.1  ankyrin repeat domain-containing protein 42 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice junction in the 5' end and differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) lacks an alternate internal aa and has a shorter and distinct C-terminus compared to isoform a.
      Source sequence(s)
      AP000873, BC045621, BU674837, EF041819
      Consensus CDS
      CCDS76457.1
      UniProtKB/TrEMBL
      A1XPJ0, F8W6I9
      Related
      ENSP00000260047.6, ENST00000260047.10
      Conserved Domains (3) summary
      cd00204
      Location:59 → 178
      ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
      sd00045
      Location:59 → 90
      ANK; ANK repeat [structural motif]
      cl25732
      Location:331 → 481
      SMC_N; RecF/RecN/SMC N terminal domain

    3. NM_001300975.2 → NP_001287904.1  ankyrin repeat domain-containing protein 42 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AP000873, BC045621, BC171752
      Consensus CDS
      CCDS76459.1
      UniProtKB/TrEMBL
      A1XPJ0, E9PIL2
      Related
      ENSP00000435790.1, ENST00000533342.6
      Conserved Domains (7) summary
      COG0666
      Location:94 → 375
      ANKYR; Ankyrin repeat [Signal transduction mechanisms]
      cd00204
      Location:59 → 179
      ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
      pfam08663
      Location:430 → 472
      HalX; HalX domain
      pfam12796
      Location:64 → 156
      Ank_2; Ankyrin repeats (3 copies)
      pfam13637
      Location:26 → 80
      Ank_4; Ankyrin repeats (many copies)
      sd00045
      Location:59 → 90
      ANK; ANK repeat [structural motif]
      cl09111
      Location:394 → 482
      Prefoldin; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits ...

    4. NM_001300976.2 → NP_001287905.1  ankyrin repeat domain-containing protein 42 isoform 5

      See identical proteins and their annotated locations for NP_001287905.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (5) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AP000873, BC045621, BX648690
      Consensus CDS
      CCDS73356.1
      UniProtKB/TrEMBL
      E9PKE2
      Related
      ENSP00000433585.1, ENST00000526731.5
      Conserved Domains (3) summary
      cd00204
      Location:59 → 179
      ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
      sd00045
      Location:59 → 90
      ANK; ANK repeat [structural motif]
      cl00748
      Location:210 → 230
      Ribosomal_L32_L32e; Ribosomal_L32_L32e: L32 is a protein from the large subunit that contains a surface-exposed globular domain and a finger-like projection that extends into the RNA core to stabilize the tertiary structure. L32 does not appear to play a role in forming the ...

    5. NM_001300977.2 → NP_001287906.1  ankyrin repeat domain-containing protein 42 isoform 6

      See identical proteins and their annotated locations for NP_001287906.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (6) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AP000873, BC045621, BX648690
      Consensus CDS
      CCDS73355.1
      UniProtKB/Swiss-Prot
      Q8N9B4
      Related
      ENSP00000377049.3, ENST00000393389.7
      Conserved Domains (2) summary
      cd00204
      Location:59 → 179
      ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
      sd00045
      Location:59 → 90
      ANK; ANK repeat [structural motif]

    6. NM_182603.4 → NP_872409.2  ankyrin repeat domain-containing protein 42 isoform 4

      See identical proteins and their annotated locations for NP_872409.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate in-frame splice junction in the 5' end and lacks an alternate exon in the 3' end compared to variant 1, that causes a frameshift. The resulting isoform (4) has a shorter and distinct C-terminus and lacks an alternate internal segment compared to isoform 1.
      Source sequence(s)
      AK095193, AP000873, BC045621
      Consensus CDS
      CCDS8265.1
      UniProtKB/Swiss-Prot
      Q49A49, Q8N9B4
      Related
      ENSP00000377051.2, ENST00000393392.6
      Conserved Domains (3) summary
      cd00204
      Location:65 → 184
      ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
      sd00045
      Location:64 → 95
      ANK; ANK repeat [structural motif]
      pfam13637
      Location:30 → 85
      Ank_4; Ankyrin repeats (many copies)

    RNA

    1. NR_125355.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) uses an alternate splice junction at the 3' end of the first exon compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.
      Source sequence(s)
      AK310765, AP000873, BC045621, BX648690

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      83193712..83256099
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      83130185..83192552
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N9B4.2 GenPept UniProtKB/Swiss-Prot:Q8N9B4

    Gene LinkOut

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

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