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

Gene ID: 127002, updated on 5-Mar-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (109483905..109492804)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (109516680..109525579)
105.20220307 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
  • 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. New loci associated with kidney function and chronic kidney disease. Köttgen A, et al. Nat Genet, 2010 May. PMID 20383146, Free PMC Article
  3. Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Vermeulen M, et al. Cell, 2010 Sep 17. PMID 20850016
  4. A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Lim J, et al. Cell, 2006 May 19. PMID 16713569
  5. Defining the human deubiquitinating enzyme interaction landscape. Sowa ME, et al. Cell, 2009 Jul 23. PMID 19615732, Free PMC Article

See all (21) 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_2023_10

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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