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

Gene ID: 646658, updated on 5-Mar-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 integral component of membrane. Predicted to be active in intracellular membrane-bounded organelle and membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Low expression observed in reference dataset See more
Orthologs
mouse all
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Genomic context

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Location:
14q24.3
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (74405899..74480143, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (68613779..68683890, complement)
105.20220307 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
  • 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_2023_10

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

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