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    SUSD1 sushi domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 64420, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SUSD1provided by HGNC
    Official Full Name
    sushi domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:25413
    See related
    Ensembl:ENSG00000106868 AllianceGenome:HGNC:25413
    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
    Summary
    Predicted to enable calcium ion binding activity. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in placenta (RPKM 5.9), urinary bladder (RPKM 5.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SUSD1 in Genome Data Viewer
    Location:
    9q31.3-q32
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (112040783..112175297, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (124212182..124346454, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (114803063..114937577, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28806 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28807 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28808 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28809 Neighboring gene RNA, U6 small nuclear 710, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28810 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28811 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28812 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28813 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28814 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28815 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:114803347-114804546 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28816 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28817 Neighboring gene long intergenic non-protein coding RNA 2977 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_106077 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28818 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28819 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:114854003-114854649 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_106106 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:114860013-114860932 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:114860933-114861851 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:114882774-114883345 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:114906608-114907807 Neighboring gene RNA, U6 small nuclear 855, pseudogene Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:114928255-114928756 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:114928757-114929256 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20188 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28820 Neighboring gene ribosomal protein L29 pseudogene 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28821 Neighboring gene polypyrimidine tract binding protein 3 Neighboring gene RNA, 7SL, cytoplasmic 57, pseudogene Neighboring gene RNA, 5S ribosomal pseudogene 295

    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 genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data. Schymick JC, et al. Lancet Neurol, 2007 Apr. PMID 17362836
    2. A genome-wide association study for venous thromboembolism: the extended cohorts for heart and aging research in genomic epidemiology (CHARGE) consortium. Tang W, et al. Genet Epidemiol, 2013 Jul. PMID 23650146, Free PMC Article
    3. Follow-up association studies of chromosome region 9q and nonsyndromic cleft lip/palate. Letra A, et al. Am J Med Genet A, 2010 Jul. PMID 20583170, Free PMC Article
    4. Elucidation of N-glycosylation sites on human platelet proteins: a glycoproteomic approach. Lewandrowski U, et al. Mol Cell Proteomics, 2006 Feb. PMID 16263699
    5. N(6)-Methyladenosine on mRNA facilitates a phase-separated nuclear body that suppresses myeloid leukemic differentiation. Cheng Y, et al. Cancer Cell, 2021 Jul 12. PMID 34048709, Free PMC Article

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: Follow-up association studies of chromosome region 9q and nonsyndromic cleft lip/palate.
    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
    A genome-wide association study for venous thromboembolism: the extended cohorts for heart and aging research in genomic epidemiology (CHARGE) consortium.
    EBI GWAS Catalog
    Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    sushi domain-containing protein 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_001282640.2 → NP_001269569.1  sushi domain-containing protein 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001269569.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AL138756, BC021125, BC060770, DB221801
      Consensus CDS
      CCDS65106.1
      UniProtKB/TrEMBL
      H3BLV4
      Related
      ENSP00000363382.2, ENST00000374264.6
      Conserved Domains (3) summary
      cd00033
      Location:179 → 235
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
      smart00179
      Location:125 → 156
      EGF_CA; Calcium-binding EGF-like domain
      pfam12947
      Location:42 → 69
      EGF_3; EGF domain

    2. NM_001282643.2 → NP_001269572.1  sushi domain-containing protein 1 isoform 3 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks two alternate exons in the 3' coding region compare to variant 1. The encoded isoform (3) is shorter and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AK056704, AL138756, AL158824, AY358746, BM998810
      Consensus CDS
      CCDS65105.1
      UniProtKB/TrEMBL
      F8WAQ1, H3BLV4
      Related
      ENSP00000363381.3, ENST00000374263.7
      Conserved Domains (3) summary
      cd00033
      Location:179 → 235
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
      smart00179
      Location:125 → 156
      EGF_CA; Calcium-binding EGF-like domain
      pfam12947
      Location:42 → 69
      EGF_3; EGF domain

    3. NM_022486.5 → NP_071931.2  sushi domain-containing protein 1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_071931.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in the 3' coding region compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus compare to isoform 1.
      Source sequence(s)
      AK292868, AL138756, AY358746, BC021125
      Consensus CDS
      CCDS6783.1
      UniProtKB/Swiss-Prot
      A1A4C5, A8KA03, Q5T8V6, Q5T8V7, Q6P9G7, Q6UWL2, Q8WU83, Q96DM9, Q9H6V2, Q9NTA7
      UniProtKB/TrEMBL
      H3BLV4
      Related
      ENSP00000363388.4, ENST00000374270.8
      Conserved Domains (3) summary
      cd00033
      Location:179 → 235
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
      smart00179
      Location:125 → 156
      EGF_CA; Calcium-binding EGF-like domain
      pfam12947
      Location:42 → 69
      EGF_3; EGF 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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      112040783..112175297 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047423727.1 → XP_047279683.1  sushi domain-containing protein 1 isoform X6

    2. XM_017015037.2 → XP_016870526.1  sushi domain-containing protein 1 isoform X5

      UniProtKB/TrEMBL
      H3BLV4

    3. XM_011518916.3 → XP_011517218.1  sushi domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      H3BLV4
      Conserved Domains (3) summary
      cd00033
      Location:179 → 235
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
      smart00179
      Location:125 → 156
      EGF_CA; Calcium-binding EGF-like domain
      pfam12947
      Location:42 → 69
      EGF_3; EGF domain

    4. XM_047423728.1 → XP_047279684.1  sushi domain-containing protein 1 isoform X7

    5. XM_047423725.1 → XP_047279681.1  sushi domain-containing protein 1 isoform X3

    6. XM_047423726.1 → XP_047279682.1  sushi domain-containing protein 1 isoform X4

    7. XM_047423724.1 → XP_047279680.1  sushi domain-containing protein 1 isoform X1

    8. XM_017015040.2 → XP_016870529.1  sushi domain-containing protein 1 isoform X8

    RNA

    1. XR_007061338.1 RNA Sequence

    2. XR_007061340.1 RNA Sequence

    3. XR_007061339.1 RNA Sequence

    4. XR_929835.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      124212182..124346454 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054363547.1 → XP_054219522.1  sushi domain-containing protein 1 isoform X6

    2. XM_054363546.1 → XP_054219521.1  sushi domain-containing protein 1 isoform X5

    3. XM_054363543.1 → XP_054219518.1  sushi domain-containing protein 1 isoform X2

    4. XM_054363548.1 → XP_054219523.1  sushi domain-containing protein 1 isoform X7

    5. XM_054363544.1 → XP_054219519.1  sushi domain-containing protein 1 isoform X3

    6. XM_054363545.1 → XP_054219520.1  sushi domain-containing protein 1 isoform X4

    7. XM_054363542.1 → XP_054219517.1  sushi domain-containing protein 1 isoform X1

    8. XM_054363549.1 → XP_054219524.1  sushi domain-containing protein 1 isoform X8

    RNA

    1. XR_008488059.1 RNA Sequence

    2. XR_008488061.1 RNA Sequence

    3. XR_008488060.1 RNA Sequence

    4. XR_008488062.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6UWL2.1 GenPept UniProtKB/Swiss-Prot:Q6UWL2

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