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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
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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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