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SERPINA2 serpin family A member 2 (gene/pseudogene) [ Homo sapiens (human) ]

Gene ID: 390502, updated on 23-Nov-2023

Summary

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Official Symbol
SERPINA2provided by HGNC
Official Full Name
serpin family A member 2 (gene/pseudogene)provided by HGNC
Primary source
HGNC:HGNC:8985
See related
Ensembl:ENSG00000258597 MIM:107410; AllianceGenome:HGNC:8985
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
ATR; PIL; ARGS; psiATR; SERPINA2P
Summary
This gene encodes a member of the serpin family of proteins, a group of proteins that inhibit serine proteases. The encoded intracellular glycoprotein is localized at the endoplasmic reticulum. This gene is a polymorphic pseudogene, with the non-functional allele being predominant in some populations. Some individuals, as represented by the reference genome allele, contain a 2kb coding region deletion and a start code mutation. [provided by RefSeq, Feb 2014]
Annotation information
Note: Genetic polymorphisms result in both protein coding and non-coding alleles of this gene.
Note: Population studies indicate that this gene is polymorphic. Deletions, frameshift mutations and a critical start codon mutation (ATG->ATA) have been found in some populations as well as an allele that can encode a functional protein. This gene may be an evolving pseudogene (PMID: 17135331). The reference genome contains the start codon mutation and has a coding region deletion. The NCBI RefSeq Project therefore treats this as a pseudogene. [13 Feb 2013]
Expression
Low expression observed in reference dataset See more
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Genomic context

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See SERPINA2 in Genome Data Viewer
Location:
14q32.13
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (94364318..94366702, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (88593837..88596220, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (94830655..94833039, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene serpin family A member 10 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:94757989-94758488 Neighboring gene serpin family A member 6 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:94812301-94813500 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:94828015-94828515 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr14:94839554-94840753 Neighboring gene serpin family A member 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:94856427-94856928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:94856929-94857428 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:94917415-94918091 Neighboring gene serpin family A member 11

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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Related articles in PubMed

  1. Sequence diversity at the proximal 14q32.1 SERPIN subcluster: evidence for natural selection favoring the pseudogenization of SERPINA2. Seixas S, et al. Mol Biol Evol, 2007 Feb. PMID 17135331
  2. Cloning and characterization of an alpha 1-antitrypsin like gene 12 KB downstream of the genuine alpha 1-antitrypsin gene. Hofker MH, et al. Biochem Biophys Res Commun, 1988 Sep 15. PMID 2901833
  3. Molecular structure and sequence homology of a gene related to alpha 1-antitrypsin in the human genome. Bao JJ, et al. Genomics, 1988 Feb. PMID 2842251
  4. The human alpha-1-antitrypsin-related sequence gene: isolation and investigation of its expression. Kelsey GD, et al. Ann Hum Genet, 1988 May. PMID 2470331
  5. Organization and expression of the human serpin gene cluster at 14q32.1. Marsden MD, et al. Front Biosci, 2005 May 1. PMID 15769666

See all (15) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Specific features of SERPINA2 include the absence of insoluble aggregates and the insignificant response to cell stress, suggesting that it is a non-polymerogenic protein with divergent activity of SERPINA1.
    Title: SERPINA2 is a novel gene with a divergent function from SERPINA1.
  2. Observational study of gene-disease association. (HuGE Navigator)
    Title: A linkage disequilibrium between genes at the serine protease inhibitor gene cluster on chromosome 14q32.1 is associated with Wegener's granulomatosis.
  3. Clinical trial and genome-wide association study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Molecular genetics of successful smoking cessation: convergent genome-wide association study results.
  4. Study found that a common haplotype in Africa had a 2-kb deletion in the SERPINA2 gene is associated with remarkable long-range homozygozity as if it was quickly driven to high frequency by natural selection acting on an advantageous variant.
    Title: Sequence diversity at the proximal 14q32.1 SERPIN subcluster: evidence for natural selection favoring the pseudogenization of SERPINA2.
Submit: New GeneRIF Correction

Phenotypes

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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

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp160, precursor env Alpha1-Antitrypsin (alpha(1)AT) is cleaved by serine proteases, causing a conformational change in alpha(1)AT that sequesters HIV-1 protease, blocks both HIV-1 gp160 and p55 processing, and is a powerful inhibitor of HIV replication PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables serine-type endopeptidase inhibitor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in negative regulation of endopeptidase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
alpha-1-antitrypsin-related protein
Names
AAT-related protein
alpha-1 antitrypsin-related protein
putative alpha-1-antitrypsin-related protein
serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 2
serpin A2
serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 2, pseudogene

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_006220.3 → NP_006211.2  alpha-1-antitrypsin-related protein precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the protein coding transcript. This allele is not found in the reference genome.
    Source sequence(s)
    AC235087
    UniProtKB/Swiss-Prot
    A0A0G2JPK4, P20848, S4UD68
    Conserved Domains (1) summary
    smart00093
    Location:62 → 418
    SERPIN; SERine Proteinase INhibitors

RNA

  1. NR_110563.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2, non-coding) represents the non-protein coding transcript. The non-coding allele, found in the reference genome, contains a 2 kb deletion and a start codon mutation when compared to the protein coding allele.
    Source sequence(s)
    AL117259
    Related
    ENST00000553483.4

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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    94364318..94366702 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187601.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    1478202..1488979 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    88593837..88596220 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NG_032041.1: Suppressed sequence

    Description
    NG_032041.1: This RefSeq was permanently suppressed because it is now thought that this gene does encode a protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P20848.2 GenPept UniProtKB/Swiss-Prot:P20848

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Miscellaneous