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DGCR2 DiGeorge syndrome critical region gene 2 [ Homo sapiens (human) ]

Gene ID: 9993, updated on 5-Aug-2018

Summary

Official Symbol
DGCR2provided by HGNC
Official Full Name
DiGeorge syndrome critical region gene 2provided by HGNC
Primary source
HGNC:HGNC:2845
See related
Ensembl:ENSG00000070413 MIM:600594; Vega:OTTHUMG00000150141
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
IDD; LAN; DGS-C; SEZ-12
Summary
Deletions of the 22q11.2 have been associated with a wide range of developmental defects (notably DiGeorge syndrome, velocardiofacial syndrome, conotruncal anomaly face syndrome and isolated conotruncal cardiac defects) classified under the acronym CATCH 22. The DGCR2 gene encodes a novel putative adhesion receptor protein, which could play a role in neural crest cells migration, a process which has been proposed to be altered in DiGeorge syndrome. Alternative splicing results in multiple transcript variants.[provided by RefSeq, May 2010]
Expression
Ubiquitous expression in brain (RPKM 24.0), skin (RPKM 23.8) and 25 other tissues See more
Orthologs

Genomic context

See DGCR2 in Genome Data Viewer
Location:
22q11.21
Exon count:
11
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 22 NC_000022.11 (19036282..19122454, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (19023795..19109967, complement)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene DiGeorge syndrome critical region gene 5 Neighboring gene DiGeorge syndrome critical region gene 10 Neighboring gene carbonic anhydrase 15, pseudogene 1 Neighboring gene ribosomal protein L28 pseudogene Neighboring gene DiGeorge syndrome critical region gene 11 Neighboring gene testis specific serine kinase 1A, pseudogene Neighboring gene testis specific serine kinase 2 Neighboring gene ess-2 splicing factor homolog

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0163, DKFZp686I1730

Gene Ontology Provided by GOA

Function Evidence Code Pubs
carbohydrate binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
animal organ morphogenesis TAS
Traceable Author Statement
more info
PubMed 
cell adhesion IEA
Inferred from Electronic Annotation
more info
 
cognition IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
integral membrane protein DGCR2/IDD
Names
DiGeorge syndrome critical region protein 2
integral membrane protein deleted in DiGeorge syndrome

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.

Genomic

  1. NG_021333.1 RefSeqGene

    Range
    5001..91173
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001173533.1NP_001167004.1  integral membrane protein DGCR2/IDD isoform 2 precursor

    See identical proteins and their annotated locations for NP_001167004.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.
    Source sequence(s)
    AK304382, AW502246, BC040500, DA494775
    Consensus CDS
    CCDS54496.1
    UniProtKB/Swiss-Prot
    P98153
    UniProtKB/TrEMBL
    Q8IWC8
    Related
    ENSP00000440062.1, ENST00000537045.5
    Conserved Domains (3) summary
    cd03599
    Location:74226
    CLECT_DGCR2_like; C-type lectin-like domain (CTLD) of the type found in DGCR2, an integral membrane protein deleted in DiGeorge Syndrome (DGS)
    smart00214
    Location:230291
    VWC; von Willebrand factor (vWF) type C domain
    pfam04534
    Location:385433
    Herpes_UL56; Herpesvirus UL56 protein
  2. NM_001173534.1NP_001167005.1  integral membrane protein DGCR2/IDD isoform 3 precursor

    See identical proteins and their annotated locations for NP_001167005.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon and uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The resulting isoform (3) lacks two internal segments, compared to isoform 1.
    Source sequence(s)
    AK296337, AW502246, BC032430, BC040500, DA494775
    UniProtKB/Swiss-Prot
    P98153
    UniProtKB/TrEMBL
    B7Z3T5, Q8IWC8
    Conserved Domains (3) summary
    cd03599
    Location:71223
    CLECT_DGCR2_like; C-type lectin-like domain (CTLD) of the type found in DGCR2, an integral membrane protein deleted in DiGeorge Syndrome (DGS)
    smart00214
    Location:227288
    VWC; von Willebrand factor (vWF) type C domain
    pfam04534
    Location:382430
    Herpes_UL56; Herpesvirus UL56 protein
  3. NM_001184781.1NP_001171710.1  integral membrane protein DGCR2/IDD isoform 4 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The resulting isoform (4) lacks a short internal segment, compared to isoform 1.
    Source sequence(s)
    AK296337, AW502246, CR936871, DA494775
    UniProtKB/TrEMBL
    B7Z3T5, Q5CZ70
    Related
    ENSP00000445069.2, ENST00000545799.5
    Conserved Domains (4) summary
    cd03599
    Location:112264
    CLECT_DGCR2_like; C-type lectin-like domain (CTLD) of the type found in DGCR2, an integral membrane protein deleted in DiGeorge Syndrome (DGS)
    smart00214
    Location:268326
    VWC; von Willebrand factor (vWF) type C domain
    cd00112
    Location:3066
    LDLa; Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about ...
    pfam04554
    Location:420459
    Extensin_2; Extensin-like region
  4. NM_005137.2NP_005128.1  integral membrane protein DGCR2/IDD isoform 1 precursor

    See identical proteins and their annotated locations for NP_005128.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AW502246, BC040500, D79985, DA494775
    Consensus CDS
    CCDS33598.1
    UniProtKB/Swiss-Prot
    P98153
    UniProtKB/TrEMBL
    Q8IWC8
    Related
    ENSP00000263196.7, OTTHUMP00000196406, ENST00000263196.11, OTTHUMT00000316504
    Conserved Domains (4) summary
    cd03599
    Location:115267
    CLECT_DGCR2_like; C-type lectin-like domain (CTLD) of the type found in DGCR2, an integral membrane protein deleted in DiGeorge Syndrome (DGS)
    smart00214
    Location:271329
    VWC; von Willebrand factor (vWF) type C domain
    cd00112
    Location:3066
    LDLa; Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about ...
    cl26464
    Location:428537
    Atrophin-1; Atrophin-1 family

RNA

  1. NR_033674.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an alternate in-frame exon and uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, which results in a frameshift and early stop codon. The transcript is sufficiently abundant to represent as a RefSeq record; however, the predicted protein is not represented because the product is significantly truncated and the transcript is a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK295697, AW502246, CR936871, DA494775

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p12 Primary Assembly

    Range
    19036282..19122454 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_001755405.1 RNA Sequence

  2. XR_001755406.2 RNA Sequence

    Related
    ENST00000389262.8
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