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

Gene ID: 338699, updated on 2-Nov-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 active in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in testis (RPKM 10.9), thyroid (RPKM 3.7) and 24 other tissues See more
Orthologs
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (83193712..83256099)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (83130185..83192552)
RS_2024_09 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 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. Genome-wide CRISPR screening identifies the pivotal role of ANKRD42 in colorectal cancer metastasis through EMT regulation. Liu S, et al. IUBMB Life, 2024 Oct. PMID 38822625
  2. 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
  3. Identification of the human testis protein phosphatase 1 interactome. Fardilha M, et al. Biochem Pharmacol, 2011 Nov 15. PMID 21382349
  4. 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
  5. Upregulation of RIN3 induces endosomal dysfunction in Alzheimer's disease. Shen R, et al. Transl Neurodegener, 2020 Jun 18. PMID 32552912, Free PMC Article

See all (11) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Genome-wide CRISPR screening identifies the pivotal role of ANKRD42 in colorectal cancer metastasis through EMT regulation.
    Title: Genome-wide CRISPR screening identifies the pivotal role of ANKRD42 in colorectal cancer metastasis through EMT regulation.
  2. the cloning and characterization of a new protein, termed SARP (several ankyrin repeat protein), which is shown to interact with all isoforms of PP1 by a variety of techniques.
    Title: SARP, a new alternatively spliced protein phosphatase 1 and DNA interacting protein.
Submit: New GeneRIF Correction

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
  
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_001433541.1 → NP_001420470.1  ankyrin repeat domain-containing protein 42 isoform 7

    Status: VALIDATED

    Source sequence(s)
    AP000873

  7. 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_2024_08

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

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