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    UBAC2 UBA domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 337867, updated on 3-Apr-2024

    Summary

    Official Symbol
    UBAC2provided by HGNC
    Official Full Name
    UBA domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:20486
    See related
    Ensembl:ENSG00000134882 AllianceGenome:HGNC:20486
    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
    PHGDHL1
    Summary
    Involved in negative regulation of canonical Wnt signaling pathway and negative regulation of retrograde protein transport, ER to cytosol. Acts upstream of or within protein localization to endoplasmic reticulum. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in testis (RPKM 8.2), thyroid (RPKM 7.2) and 25 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See UBAC2 in Genome Data Viewer
    Location:
    13q32.3
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (99200854..99386504)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (98411009..98596811)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (99853108..100038758)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:99852081-99852734 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:99852735-99853386 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5469 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:99854040-99854691 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7931 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:99857838-99858338 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 22 Neighboring gene UBAC2 antisense RNA 1 Neighboring gene RN7SK pseudogene 9 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7932 Neighboring gene H2A.Z histone pseudogene 3 Neighboring gene uncharacterized LOC124903198 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:99914553-99914775 Neighboring gene G protein-coupled receptor 18 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5470 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:99955752-99956300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:99956301-99956847 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr13:99966417-99967616 Neighboring gene G protein-coupled receptor 183 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:99994828-99995328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:99995329-99995829 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7934 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7935 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7937 Neighboring gene FKSG29 Neighboring gene microRNA 623 Neighboring gene Sharpr-MPRA regulatory region 8816 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100037611-100038229 Neighboring gene high mobility group box 3 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100069445-100070364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7940 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7941 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7942 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7943 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7945 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr13:100084644-100085843 Neighboring gene C-C motif chemokine receptor 12, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7947 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100105623-100106122 Neighboring gene Sharpr-MPRA regulatory region 5830 Neighboring gene MPRA-validated peak2103 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:100147579-100148093 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7948 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7950 Neighboring gene long intergenic non-protein coding RNA 1232

    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

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies novel alleles associated with risk of cutaneous basal cell carcinoma and squamous cell carcinoma.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ26351, FLJ30001, FLJ30548, FLJ42413, MGC90487

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    ubiquitin-associated domain-containing protein 2
    Names
    RP11-178C10.1
    UBA domain-containing protein 2
    phosphoglycerate dehydrogenase like 1
    phosphoglycerate dehydrogenase-like protein 1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001144072.2NP_001137544.1  ubiquitin-associated domain-containing protein 2 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001137544.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AI866141, AK075419, AK290342, AL136961, BC072674
      Consensus CDS
      CCDS45064.1
      UniProtKB/Swiss-Prot
      B3KNV7, Q0VAB5, Q5W0W6, Q5W0W9, Q6GQR2, Q6P4B0, Q8N2E8, Q8NBM4, Q96NW2
      UniProtKB/TrEMBL
      A8K2S7
      Related
      ENSP00000383911.3, ENST00000403766.8
      Conserved Domains (1) summary
      cd14305
      Location:305342
      UBA_UBAC2; UBA domain found in ubiquitin-associated domain-containing protein 2 (UBAC2) and similar proteins
    2. NM_177967.4NP_808882.1  ubiquitin-associated domain-containing protein 2 isoform 2

      See identical proteins and their annotated locations for NP_808882.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate 5' end exon and is missing two consecutive in-frame coding exons compared to transcript variant 1. This results in a shorter isoform (2) with a different N-terminus compares to isoform 1.
      Source sequence(s)
      AI866141, AK054563, AL136961, AL159981, BC072674
      Consensus CDS
      CCDS9490.1
      UniProtKB/Swiss-Prot
      Q8NBM4
      Related
      ENSP00000365623.2, ENST00000376440.6
      Conserved Domains (1) summary
      cd14305
      Location:270307
      UBA_UBAC2; UBA domain found in ubiquitin-associated domain-containing protein 2 (UBAC2) and similar proteins

    RNA

    1. NR_026644.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains an alternate 5' end exon compared to transcript variant 1, which results in use of downstream translation start site and premature translation termination, rendering this transcript susceptible to nonsense-mediated mRNA decay (NMD). This transcript is sufficiently abundant to represent as a RefSeq record, however, the predicted protein is not represented because it is significantly truncated.
      Source sequence(s)
      AI866141, AK054563, AL136961, AL159981, BC072674, BC121139

    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_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      99200854..99386504
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011521083.3XP_011519385.1  ubiquitin-associated domain-containing protein 2 isoform X2

      Conserved Domains (1) summary
      cd14305
      Location:253290
      UBA_UBAC2; UBA domain found in ubiquitin-associated domain-containing protein 2 (UBAC2) and similar proteins
    2. XM_011521082.3XP_011519384.2  ubiquitin-associated domain-containing protein 2 isoform X1

    3. XM_047430286.1XP_047286242.1  ubiquitin-associated domain-containing protein 2 isoform X3

      Related
      ENST00000494576.5
    4. XM_017020553.2XP_016876042.1  ubiquitin-associated domain-containing protein 2 isoform X4

      Conserved Domains (1) summary
      cd14305
      Location:135172
      UBA_UBAC2; UBA domain found in ubiquitin-associated domain-containing protein 2 (UBAC2) and similar proteins

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      98411009..98596811
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054374488.1XP_054230463.1  ubiquitin-associated domain-containing protein 2 isoform X2

    2. XM_054374487.1XP_054230462.1  ubiquitin-associated domain-containing protein 2 isoform X1

    3. XM_054374489.1XP_054230464.1  ubiquitin-associated domain-containing protein 2 isoform X3

    4. XM_054374490.1XP_054230465.1  ubiquitin-associated domain-containing protein 2 isoform X4