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    SYNDIG1L synapse differentiation inducing 1 like [ Homo sapiens (human) ]

    Gene ID: 646658, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SYNDIG1Lprovided by HGNC
    Official Full Name
    synapse differentiation inducing 1 likeprovided by HGNC
    Primary source
    HGNC:HGNC:32388
    See related
    Ensembl:ENSG00000183379 MIM:609999; AllianceGenome:HGNC:32388
    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
    DSPC1; CAPUCIN; IFITMD4; SynDIG2; TMEM90A
    Summary
    Predicted to be located in Golgi apparatus. Predicted to be active in intracellular membrane-bounded organelle and membrane. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    See SYNDIG1L in Genome Data Viewer
    Location:
    14q24.3
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (74405899..74480143, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (68613779..68683890, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (74872602..74892913, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene SUB1 pseudogene 2 Neighboring gene vertebrae development associated Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:74792429-74793048 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:74794289-74794910 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:74796151-74796770 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:74815437-74816187 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:74816188-74816937 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:74825115-74825693 Neighboring gene ribosomal protein S2 pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:74861891-74862391 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:74868255-74869164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:74873841-74874342 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:74876293-74876840 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:74954493-74955692 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5930 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5931 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8728 Neighboring gene microRNA 4709 Neighboring gene RAP1A, member of RAS oncogene family pseudogene Neighboring gene NPC intracellular cholesterol transporter 2 Neighboring gene iron-sulfur cluster assembly 2

    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. Capucin: a novel striatal marker down-regulated in rodent models of Huntington disease. de Chaldée M, et al. Genomics, 2006 Feb. PMID 16359841
    2. The dispanins: a novel gene family of ancient origin that contains 14 human members. Sällman Almén M, et al. PLoS One, 2012. PMID 22363774, Free PMC Article
    3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Cloning and characterization of the TMEM90A (capucin) ortholog in mouse.
      Title: Capucin: a novel striatal marker down-regulated in rodent models of Huntington disease.
    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

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in intracellular membrane-bounded organelle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    synapse differentiation-inducing gene protein 1-like
    Names
    caudate- and putamen-enriched sequence
    dispanin subfamily C member 1
    interferon induced transmembrane protein domain containing 4
    transmembrane protein 90A

    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_001105579.2 → NP_001099049.1  synapse differentiation-inducing gene protein 1-like

      See identical proteins and their annotated locations for NP_001099049.1

      Status: VALIDATED

      Source sequence(s)
      AC005479, CK906042, DB173128, DB473943
      Consensus CDS
      CCDS41970.1
      UniProtKB/Swiss-Prot
      A6NDD5
      Related
      ENSP00000331474.3, ENST00000331628.8
      Conserved Domains (1) summary
      pfam04505
      Location:157 → 217
      CD225; Interferon-induced transmembrane protein

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      74405899..74480143 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017021600.2 → XP_016877089.1  synapse differentiation-inducing gene protein 1-like isoform X1

      UniProtKB/Swiss-Prot
      A6NDD5
      Conserved Domains (1) summary
      pfam04505
      Location:157 → 217
      CD225; Interferon-induced transmembrane protein

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      68613779..68683890 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054376615.1 → XP_054232590.1  synapse differentiation-inducing gene protein 1-like isoform X1

      UniProtKB/Swiss-Prot
      A6NDD5

    2. XM_054376616.1 → XP_054232591.1  synapse differentiation-inducing gene protein 1-like isoform X1

      UniProtKB/Swiss-Prot
      A6NDD5
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A6NDD5.1 GenPept UniProtKB/Swiss-Prot:A6NDD5

    Gene LinkOut

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

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