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    ATXN7L2 ataxin 7 like 2 [ Homo sapiens (human) ]

    Gene ID: 127002, updated on 17-Sep-2024

    Summary

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    Official Symbol
    ATXN7L2provided by HGNC
    Official Full Name
    ataxin 7 like 2provided by HGNC
    Primary source
    HGNC:HGNC:28713
    See related
    Ensembl:ENSG00000162650 AllianceGenome:HGNC:28713
    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
    Expression
    Broad expression in testis (RPKM 4.6), brain (RPKM 2.1) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ATXN7L2 in Genome Data Viewer
    Location:
    1p13.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (109483905..109492804)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (109516680..109525579)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (110026527..110035426)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:109940693-109941674 Neighboring gene proteasome 20S subunit alpha 5 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:109969133-109970064 Neighboring gene MPRA-validated peak355 silencer Neighboring gene MPRA-validated peak356 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110008599-110009100 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110009101-110009600 Neighboring gene synaptophysin like 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110020155-110020674 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:110025999-110026616 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:110026617-110027236 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1151 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1441 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110036856-110037356 Neighboring gene Sharpr-MPRA regulatory region 8825 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110042111-110042610 Neighboring gene cytochrome b561 family member D1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1153 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1154 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1155 Neighboring gene adhesion molecule with Ig like domain 1

    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 association study of recurrent early-onset major depressive disorder. Shi J, et al. Mol Psychiatry, 2011 Feb. PMID 20125088, Free PMC Article
    2. ATAC and SAGA co-activator complexes utilize co-translational assembly, but their cellular localization properties and functions are distinct. Yayli G, et al. Cell Rep, 2023 Sep 26. PMID 37682711, Free PMC Article
    3. New loci associated with kidney function and chronic kidney disease. Köttgen A, et al. Nat Genet, 2010 May. PMID 20383146, Free PMC Article
    4. Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Vermeulen M, et al. Cell, 2010 Sep 17. PMID 20850016
    5. BioID identifies novel c-MYC interacting partners in cultured cells and xenograft tumors. Dingar D, et al. J Proteomics, 2015 Apr 6. PMID 25452129

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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

    EBI GWAS Catalog

    Description
    Genome-wide association study of recurrent early-onset major depressive disorder.
    EBI GWAS Catalog
    New loci associated with kidney function and chronic kidney disease.
    EBI GWAS Catalog

    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

    • FLJ00381, MGC46534

    General protein information

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    Preferred Names
    ataxin-7-like protein 2
    Names
    ataxin 7-like 1

    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_001350174.1 → NP_001337103.1  ataxin-7-like protein 2 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) includes an alternate penultimate exon, compared to variant 1, resulting in a novel 3' coding region and distinct 3' UTR. The encoded isoform (3) has a longer and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AW873529, BC036849, BC037582, BI489982, HY055086, HY089487
      Consensus CDS
      CCDS91018.1
      UniProtKB/TrEMBL
      A0A804HIT1
      Related
      ENSP00000507211.1, ENST00000459635.2
      Conserved Domains (1) summary
      pfam08313
      Location:258 → 321
      SCA7; SCA7, zinc-binding domain

    2. NM_001350175.2 → NP_001337104.1  ataxin-7-like protein 2 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes isoform 1
      Source sequence(s)
      AL355145
      Consensus CDS
      CCDS91019.1
      UniProtKB/TrEMBL
      A0A804HIX1
      Related
      ENSP00000507259.1, ENST00000683729.1
      Conserved Domains (1) summary
      pfam08313
      Location:258 → 321
      SCA7; SCA7, zinc-binding domain

    3. NM_001350177.2 → NP_001337106.1  ataxin-7-like protein 2 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains an alternate exon in the 5' region, resulting in use of a downstream start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus than isoform 1.
      Source sequence(s)
      AL355145, BC036849, BC037582, BI489982, HY051016
      Conserved Domains (1) summary
      pfam08313
      Location:200 → 263
      SCA7; SCA7, zinc-binding domain

    4. NM_153340.5 → NP_699171.3  ataxin-7-like protein 2 isoform 2

      See identical proteins and their annotated locations for NP_699171.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (2) has the same N- and C-termini, but is shorter than isoform .
      Source sequence(s)
      BC036849, BC037582, HY055086, HY089487
      Consensus CDS
      CCDS30794.1
      UniProtKB/Swiss-Prot
      Q5T6C5
      Related
      ENSP00000358886.3, ENST00000369870.7
      Conserved Domains (1) summary
      pfam08313
      Location:226 → 289
      SCA7; SCA7, zinc-binding domain

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      109483905..109492804
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047444943.1 → XP_047300899.1  ataxin-7-like protein 2 isoform X3

    2. XM_011540641.3 → XP_011538943.1  ataxin-7-like protein 2 isoform X3

      See identical proteins and their annotated locations for XP_011538943.1

      Conserved Domains (1) summary
      pfam08313
      Location:200 → 263
      SCA7; SCA7, zinc-binding domain

    3. XM_011540638.3 → XP_011538940.1  ataxin-7-like protein 2 isoform X1

      Conserved Domains (1) summary
      pfam08313
      Location:236 → 299
      SCA7; SCA7, zinc-binding domain

    4. XM_047444940.1 → XP_047300896.1  ataxin-7-like protein 2 isoform X2

    5. XM_011540646.3 → XP_011538948.1  ataxin-7-like protein 2 isoform X6

      UniProtKB/TrEMBL
      A0A804HJY2
      Related
      ENSP00000507693.1, ENST00000604728.6
      Conserved Domains (1) summary
      pfam08313
      Location:258 → 321
      SCA7; SCA7, zinc-binding domain

    6. XM_011540639.4 → XP_011538941.1  ataxin-7-like protein 2 isoform X3

      See identical proteins and their annotated locations for XP_011538941.1

      Conserved Domains (1) summary
      pfam08313
      Location:200 → 263
      SCA7; SCA7, zinc-binding domain

    7. XM_017000267.3 → XP_016855756.1  ataxin-7-like protein 2 isoform X3

      Conserved Domains (1) summary
      pfam08313
      Location:200 → 263
      SCA7; SCA7, zinc-binding domain

    8. XM_047444962.1 → XP_047300918.1  ataxin-7-like protein 2 isoform X3

    9. XM_047444974.1 → XP_047300930.1  ataxin-7-like protein 2 isoform X4

    10. XM_047444992.1 → XP_047300948.1  ataxin-7-like protein 2 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      109516680..109525579
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054334302.1 → XP_054190277.1  ataxin-7-like protein 2 isoform X3

    2. XM_054334303.1 → XP_054190278.1  ataxin-7-like protein 2 isoform X3

    3. XM_054334299.1 → XP_054190274.1  ataxin-7-like protein 2 isoform X1

    4. XM_054334300.1 → XP_054190275.1  ataxin-7-like protein 2 isoform X2

    5. XM_054334308.1 → XP_054190283.1  ataxin-7-like protein 2 isoform X6

      UniProtKB/TrEMBL
      A0A804HJY2

    6. XM_054334301.1 → XP_054190276.1  ataxin-7-like protein 2 isoform X3

    7. XM_054334304.1 → XP_054190279.1  ataxin-7-like protein 2 isoform X3

    8. XM_054334305.1 → XP_054190280.1  ataxin-7-like protein 2 isoform X3

    9. XM_054334306.1 → XP_054190281.1  ataxin-7-like protein 2 isoform X4

    10. XM_054334307.1 → XP_054190282.1  ataxin-7-like protein 2 isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5T6C5.1 GenPept UniProtKB/Swiss-Prot:Q5T6C5

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