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SLAIN1 SLAIN motif family member 1 [ Homo sapiens (human) ]

Gene ID: 122060, updated on 3-Apr-2024

Summary

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Official Symbol
SLAIN1provided by HGNC
Official Full Name
SLAIN motif family member 1provided by HGNC
Primary source
HGNC:HGNC:26387
See related
Ensembl:ENSG00000139737 MIM:610491; AllianceGenome:HGNC:26387
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
C13orf32
Summary
Predicted to be located in cytoplasm and cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in brain (RPKM 39.3), testis (RPKM 10.8) and 7 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
13q22.3
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (77697687..77764229)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (76922360..76989219)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (78271822..78338364)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene putative UPF0607 protein ENSP00000383144 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:78237303-78237481 Neighboring gene serine palmitoyltransferase long chain base subunit 1 pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5420 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5421 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5422 Neighboring gene microRNA 3665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7846 Neighboring gene NANOG hESC enhancer GRCh37_chr13:78358462-78359034 Neighboring gene EDNRB antisense RNA 1 Neighboring gene VISTA enhancer hs1394 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:78425667-78426299 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:78427507-78428016 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:78428017-78428526 Neighboring gene EDNRB proximal promoter region Neighboring gene endothelin receptor type B Neighboring gene RNA, 7SL, cytoplasmic 810, pseudogene

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Expressed at the stem cell and epiblast stages of embryonic stem cell differentiation.
    Title: Transcriptional profiling of mouse and human ES cells identifies SLAIN1, a novel stem cell gene.
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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ30046, MGC131899

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cytoplasmic microtubule organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in microtubule nucleation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of microtubule polymerization IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
colocalizes_with microtubule plus-end IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
SLAIN motif-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_001040153.4 → NP_001035243.2  SLAIN motif-containing protein 1 isoform A

    See identical proteins and their annotated locations for NP_001035243.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes isoform A.
    Source sequence(s)
    AK294201, BC045177
    Consensus CDS
    CCDS31995.2
    UniProtKB/TrEMBL
    A0A0C4DFN6
    Related
    ENSP00000418707.1, ENST00000488699.5
    Conserved Domains (1) summary
    pfam15301
    Location:46 → 426
    SLAIN; SLAIN motif-containing family

  2. NM_001242868.2 → NP_001229797.1  SLAIN motif-containing protein 1 isoform C

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate 5' exon, and thus differs in the 5' UTR and 5' coding region, compared to variant 1. The encoded isoform (C) has a distinct and longer N-terminus, compared to isoform A.
    Source sequence(s)
    AL354831, BC045177, BG391962, BQ433296, DB500463
    Consensus CDS
    CCDS73588.1
    UniProtKB/Swiss-Prot
    A8K0Z9, B7Z209, Q5T6P4, Q5T6P7, Q8ND10, Q8ND83, Q96NV0
    UniProtKB/TrEMBL
    A0A0A0MSS3
    Related
    ENSP00000400921.2, ENST00000418532.6
    Conserved Domains (1) summary
    pfam15301
    Location:209 → 590
    SLAIN; SLAIN motif-containing family

  3. NM_001242869.2 → NP_001229798.1  SLAIN motif-containing protein 1 isoform D

    See identical proteins and their annotated locations for NP_001229798.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, uses a downstream in-frame start codon, and lacks an internal in-frame coding exon, compared to variant 1. The encoded isoform (D) is shorter at the N-terminus and lacks an internal segment, compared to isoform A. Both variants 4 and 5 encode isoform D.
    Source sequence(s)
    AK289600, DA096260, DA343547
    Consensus CDS
    CCDS55901.1
    UniProtKB/Swiss-Prot
    Q8ND83
    Related
    ENSP00000314443.5, ENST00000314070.9
    Conserved Domains (1) summary
    pfam15301
    Location:20 → 191
    SLAIN; SLAIN motif-containing family

  4. NM_001242870.2 → NP_001229799.1  SLAIN motif-containing protein 1 isoform D

    See identical proteins and their annotated locations for NP_001229799.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, uses a downstream in-frame start codon, and lacks an internal in-frame coding exon, compared to variant 1. The encoded isoform (D) is shorter at the N-terminus and lacks an internal segment, compared to isoform A. Both variants 4 and 5 encode isoform D.
    Source sequence(s)
    AL834203, DA343547
    Consensus CDS
    CCDS55901.1
    UniProtKB/Swiss-Prot
    Q8ND83
    Conserved Domains (1) summary
    pfam15301
    Location:20 → 191
    SLAIN; SLAIN motif-containing family

  5. NM_001242871.2 → NP_001229800.1  SLAIN motif-containing protein 1 isoform E

    See identical proteins and their annotated locations for NP_001229800.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR, lacks a portion of the 5' coding region, uses an alternate start codon, and includes an alternate splice site in its 5' coding region, compared to variant 1. The encoded isoform (E) has a distinct and shorter N-terminus, compared to isoform A.
    Source sequence(s)
    AK295423, BC045177, DA343547
    Consensus CDS
    CCDS73589.1
    UniProtKB/TrEMBL
    A0A0C4DFN6, B7Z326
    Related
    ENSP00000314546.8, ENST00000351546.7
    Conserved Domains (1) summary
    pfam15301
    Location:21 → 304
    SLAIN; SLAIN motif-containing family

  6. NM_001366665.1 → NP_001353594.1  SLAIN motif-containing protein 1 isoform F

    Status: VALIDATED

    Source sequence(s)
    AL354831
    Consensus CDS
    CCDS91821.1
    UniProtKB/TrEMBL
    A0A994J5K0
    Related
    ENSP00000516138.1, ENST00000705543.1
    Conserved Domains (1) summary
    pfam15301
    Location:46 → 476
    SLAIN; SLAIN motif-containing family

  7. NM_001366666.1 → NP_001353595.1  SLAIN motif-containing protein 1 isoform B

    Status: VALIDATED

    Source sequence(s)
    AL354831
    Consensus CDS
    CCDS9460.1
    UniProtKB/TrEMBL
    A0A0C4DFN6
    Related
    ENSP00000351507.2, ENST00000358679.3
    Conserved Domains (1) summary
    pfam15301
    Location:1 → 305
    SLAIN; SLAIN motif-containing family

  8. NM_001411026.1 → NP_001397955.1  SLAIN motif-containing protein 1 isoform G

    Status: VALIDATED

    Description
    Transcript Variant: This variant (9) represents the allele encoded by the GRCh38 reference genome and encodes isoform (G).
    Source sequence(s)
    AL354831
    Consensus CDS
    CCDS91820.1
    UniProtKB/TrEMBL
    Q5T6P1
    Related
    ENSP00000403049.2, ENST00000446759.6

  9. NM_001412123.1 → NP_001399052.1  SLAIN motif-containing protein 1 isoform H

    Status: VALIDATED

    Source sequence(s)
    CP068265

  10. NM_001412125.1 → NP_001399054.1  SLAIN motif-containing protein 1 isoform I

    Status: VALIDATED

    Description
    Transcript Variant: This variant (11) uses the same exon combination as variant 9 but represents the allele encoded by the T2T genome assembly. The encoded isoform (I) has a slightly different sequence in the N-terminal region compared to isoform G.
    Source sequence(s)
    CP068265

  11. NM_144595.4 → NP_653196.1  SLAIN motif-containing protein 1 isoform B

    See identical proteins and their annotated locations for NP_653196.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (B) is shorter at the N-terminus, compared to isoform A.
    Source sequence(s)
    BC045177, DA343547
    Consensus CDS
    CCDS9460.1
    UniProtKB/TrEMBL
    A0A0C4DFN6
    Conserved Domains (1) summary
    pfam15301
    Location:1 → 305
    SLAIN; SLAIN motif-containing family

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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    77697687..77764229
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    76922360..76989219
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8ND83.3 GenPept UniProtKB/Swiss-Prot:Q8ND83

Gene LinkOut

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