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SHLD1 shieldin complex subunit 1 [ Homo sapiens (human) ]

Gene ID: 149840, updated on 29-Aug-2020

Summary

Official Symbol
SHLD1provided by HGNC
Official Full Name
shieldin complex subunit 1provided by HGNC
Primary source
HGNC:HGNC:26318
See related
Ensembl:ENSG00000171984 MIM:618028
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
RINN3; C20orf196
Expression
Ubiquitous expression in lymph node (RPKM 1.6), adrenal (RPKM 1.1) and 24 other tissues See more
Orthologs

Genomic context

See SHLD1 in Genome Data Viewer
Location:
20p12.3
Exon count:
11
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 20 NC_000020.11 (5750286..5864395)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (5731043..5844558)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene eukaryotic translation initiation factor 4E pseudogene 1 Neighboring gene glycerophosphocholine phosphodiesterase 1 Neighboring gene uncharacterized LOC105372514 Neighboring gene RNA, U1 small nuclear 55, pseudogene Neighboring gene chromogranin B

Genomic regions, transcripts, and products

Expression

  • 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

Phenotypes

Associated conditions

Description Tests
Whole genome association scan for genetic polymorphisms influencing information processing speed.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ25067

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
chromosome IDA
Inferred from Direct Assay
more info
PubMed 
site of double-strand break IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
site of double-strand break IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
shieldin complex subunit 1
Names
RINN1-REV7-interacting novel NHEJ regulator 3
shield complex subunit 1
uncharacterized protein C20orf196

NCBI Reference Sequences (RefSeq)

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_001303477.2NP_001290406.1  shieldin complex subunit 1 isoform 1

    See identical proteins and their annotated locations for NP_001290406.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Variants 1 and 2 encode isoform 1.
    Source sequence(s)
    AK057796, AK292708, BU656896, HY270691
    Consensus CDS
    CCDS13091.1
    UniProtKB/Swiss-Prot
    Q8IYI0
    Conserved Domains (1) summary
    pfam15021
    Location:3201
    DUF4521; Protein of unknown function (DUF4521)
  2. NM_001303478.2NP_001290407.1  shieldin complex subunit 1 isoform 2

    See identical proteins and their annotated locations for NP_001290407.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an exon in the 5' UTR, contains an alternate exon in the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct, shorter N-terminus than isoform 1.
    Source sequence(s)
    AK057796, AK292708, AL390028, HY080554, HY270691
    UniProtKB/Swiss-Prot
    Q8IYI0
    Conserved Domains (1) summary
    pfam15021
    Location:21169
    DUF4521; Protein of unknown function (DUF4521)
  3. NM_001303479.2NP_001290408.1  shieldin complex subunit 1 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an exon in the 5' UTR and contains an alternate 3' terminal exon, resulting in a different 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (3) has a distinct, shorter C-terminus than isoform 1.
    Source sequence(s)
    AK057796, AV715251
    Consensus CDS
    CCDS77565.1
    UniProtKB/Swiss-Prot
    Q8IYI0
    UniProtKB/TrEMBL
    Q5TGA6
    Related
    ENSP00000368263.4, ENST00000378979.8
    Conserved Domains (1) summary
    pfam15021
    Location:359
    DUF4521; Protein of unknown function (DUF4521)
  4. NM_152504.4NP_689717.2  shieldin complex subunit 1 isoform 1

    See identical proteins and their annotated locations for NP_689717.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an exon in the 5' UTR compared to variant 1. Variants 1 and 2 encode isoform 1.
    Source sequence(s)
    AK057796, AK292708, AL390028, HY270691
    Consensus CDS
    CCDS13091.1
    UniProtKB/Swiss-Prot
    Q8IYI0
    Related
    ENSP00000305875.6, ENST00000303142.11
    Conserved Domains (1) summary
    pfam15021
    Location:3201
    DUF4521; Protein of unknown function (DUF4521)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p13 Primary Assembly

    Range
    5750286..5864395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011529178.2XP_011527480.1  shieldin complex subunit 1 isoform X4

  2. XM_011529179.2XP_011527481.1  shieldin complex subunit 1 isoform X5

  3. XM_011529182.2XP_011527484.1  shieldin complex subunit 1 isoform X8

  4. XM_011529180.2XP_011527482.1  shieldin complex subunit 1 isoform X6

  5. XM_011529177.2XP_011527479.1  shieldin complex subunit 1 isoform X1

  6. XM_017027684.1XP_016883173.1  shieldin complex subunit 1 isoform X3

    UniProtKB/Swiss-Prot
    Q8IYI0
    Conserved Domains (1) summary
    pfam15021
    Location:3201
    DUF4521; Protein of unknown function (DUF4521)
  7. XM_011529181.3XP_011527483.1  shieldin complex subunit 1 isoform X7

  8. XM_006723549.4XP_006723612.1  shieldin complex subunit 1 isoform X2

    Conserved Domains (1) summary
    pfam15021
    Location:6202
    DUF4521; Protein of unknown function (DUF4521)
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