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BOLA2-SMG1P6 BOLA2-SMG1P6 readthrough [ Homo sapiens (human) ]

Gene ID: 107282092, updated on 10-Oct-2023

Summary

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Official Symbol
BOLA2-SMG1P6provided by HGNC
Official Full Name
BOLA2-SMG1P6 readthroughprovided by HGNC
Primary source
HGNC:HGNC:53563
See related
AllianceGenome:HGNC:53563
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
Summary
This gene represents naturally-occurring readthrough transcription between the upstream BOLA2 (bolA family member 2) and downstream SMG1 pseudogene 6 (SMG1P6) loci. Alternative splicing results in multiple transcript variants, some of which may encode proteins with an N-terminus similar to BOLA2 and a C-terminus related to SMG1 phosphatidylinositol 3-kinase-related kinase. [provided by RefSeq, Feb 2016]
Expression
Ubiquitous expression in bone marrow (RPKM 25.1), duodenum (RPKM 18.0) and 25 other tissues See more
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Genomic context

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Location:
16p11.2
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (29442905..29454964, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (29724697..29736755, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (29454226..29466285, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29393253-29393874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29393875-29394494 Neighboring gene nuclear pore complex interacting protein family member B11 Neighboring gene SMG1 pseudogene 6 Neighboring gene small nucleolar RNA U13 Neighboring gene coronin 1A pseudogene Neighboring gene SLX1B-SULT1A4 readthrough (NMD candidate) Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:29465349-29466088 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:29466829-29467566 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:29470053-29470888 Neighboring gene bolA family member 2 Neighboring gene SLX1 homolog B, structure-specific endonuclease subunit Neighboring gene sulfotransferase family 1A member 4 Neighboring gene SAGA complex associated factor 29 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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Related articles in PubMed

  1. 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
  2. A reference map of the human binary protein interactome. Luck K, et al. Nature, 2020 Apr. PMID 32296183, Free PMC Article
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039
  4. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

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 variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Clone Names

  • FLJ23602, FLJ40558, FLJ53018, MGC163273, MGC163275

General protein information

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Preferred Names
BOLA2-SMG1P6 protein
Names
BOLA2-SMG1P6 readthrough protein

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_001320622.1 → NP_001307551.1  BOLA2-SMG1P6 protein isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AC133555, AK295153, BM451872
    UniProtKB/TrEMBL
    B4DHK7

  2. NM_001320623.1 → NP_001307552.1  BOLA2-SMG1P6 protein isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses two alternate splice sites in the coding region, resulting in a region containing a frameshift, compared to variant 1. The encoded isoform (b) is shorter than isoform a.
    Source sequence(s)
    AC133555, AK295153, DA438012
    UniProtKB/TrEMBL
    B4DHK7
    Conserved Domains (1) summary
    cl00386
    Location:78 → 119
    BolA; BolA-like protein

  3. NM_001320624.1 → NP_001307553.1  BOLA2-SMG1P6 protein isoform c

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The encoded isoform (c) is shorter than isoform a.
    Source sequence(s)
    AC133555, AK295153, BG030350
    UniProtKB/TrEMBL
    B4DHK7

  4. NM_001320625.1 → NP_001307554.1  BOLA2-SMG1P6 protein isoform d

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an exon and uses an alternate splice site in the 5' coding region, and initiates translation at an alternate downstream start codon, compared to variant 1. The encoded isoform (d) has a distinct, shorter N-terminus than isoform a.
    Source sequence(s)
    AC133555, AK295153, BG282633, DA438012
    UniProtKB/TrEMBL
    B4DHK7

  5. NM_001320627.1 → NP_001307556.1  BOLA2-SMG1P6 protein isoform e

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) uses an alternate splice site in the 5' region and initiates translation at a downstream start codon compared to variant 1. The encoded isoform (e) has a shorter N-terminus than isoform a. Variants 5 and 6 encode the same isoform (e).
    Source sequence(s)
    AC133555, AK295153, BM696373
    UniProtKB/TrEMBL
    B4DHK7

  6. NM_001320628.1 → NP_001307557.1  BOLA2-SMG1P6 protein isoform e

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (e) has a shorter N-terminus than isoform a. Variants 5 and 6 encode the same isoform (e).
    Source sequence(s)
    AC133555, AK295153, BM696373
    UniProtKB/TrEMBL
    B4DHK7

RNA

  1. NR_135316.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) uses an alternate splice site and lacks an exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC133555, AK295153, BI517472

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    29442905..29454964 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    29724697..29736755 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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