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SMG1P2 SMG1 pseudogene 2 [ Homo sapiens (human) ]

Gene ID: 440354, updated on 17-Sep-2024

Summary

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Official Symbol
SMG1P2provided by HGNC
Official Full Name
SMG1 pseudogene 2provided by HGNC
Primary source
HGNC:HGNC:49859
See related
AllianceGenome:HGNC:49859
Gene type
pseudo
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Expression
Ubiquitous expression in bone marrow (RPKM 25.3), lymph node (RPKM 12.5) and 25 other tissues See more
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Genomic context

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See SMG1P2 in Genome Data Viewer
Location:
16p11.2
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (29545011..29613717, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (29827051..29895761, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (29556332..29625038, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene nuclear pore complex interacting protein family member B12 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7326 Neighboring gene uncharacterized LOC105371168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29616815-29617536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29617537-29618258 Neighboring gene microRNA 3680-2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10657 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7327 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7328 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:29625406-29626091 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:29626092-29626776 Neighboring gene solute carrier family 7 member 5 pseudogene 1 Neighboring gene carbonic anhydrase 5A pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10658 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10659 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10660 Neighboring gene Sharpr-MPRA regulatory region 12377 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10661 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10663 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10664 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7329 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7330 Neighboring gene sialophorin

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. Up-regulated expression of a novel gene in activated human peripheral blood mononuclear cells that is a truncated paralog of the human system L-amino acid transporter 1. Ito M, et al. Int J Biochem Cell Biol, 2002 Sep. PMID 12009310
  2. RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination. Choudhury NR, et al. BMC Biol, 2017 Nov 8. PMID 29117863, Free PMC Article
  3. VIRMA mediates preferential m(6)A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. Yue Y, et al. Cell Discov, 2018. PMID 29507755, Free PMC Article
  4. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

See all (6) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Other Names

  • SMG1P2, nonsense mediated mRNA decay associated PI3K related kinase pseudogene 2
  • smg-1 homolog, phosphatidylinositol 3-kinase-related kinase pseudogene

Clone Names

  • FLJ18576

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.

RNA

  1. NR_135305.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an exon and contains two alternate 5' exons and an alternate internal exon, and is shorter than variant 1.
    Source sequence(s)
    AK097897, AK304513, AW182584, DA936903, DB143721

  2. NR_135317.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript.
    Source sequence(s)
    AC009086

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    29545011..29613717 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_017852933.1 Reference GRCh38.p14 PATCHES

    Range
    1584375..1641260
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    29827051..29895761 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NR_002473.2: Suppressed sequence

    Description
    NR_002473.2: This RefSeq was removed because currently there is support for the transcript.
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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