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HMGXB4 HMG-box containing 4 [ Homo sapiens (human) ]

Gene ID: 10042, updated on 9-Feb-2020

Summary

Official Symbol
HMGXB4provided by HGNC
Official Full Name
HMG-box containing 4provided by HGNC
Primary source
HGNC:HGNC:5003
See related
Ensembl:ENSG00000100281 MIM:604702
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
HMG2L1; HMGBCG; THC211630
Summary
High mobility group (HMG) proteins are nonhistone chromosomal proteins. See HMG2 (MIM 163906) for additional information on HMG proteins.[supplied by OMIM, Nov 2010]
Expression
Ubiquitous expression in testis (RPKM 8.3), bone marrow (RPKM 7.9) and 25 other tissues See more
Orthologs

Genomic context

See HMGXB4 in Genome Data Viewer
Location:
22q12.3
Exon count:
12
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 22 NC_000022.11 (35256697..35295807)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (35653445..35691800)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1399 Neighboring gene cytochrome c oxidase subunit 7B pseudogene 1 Neighboring gene uncharacterized LOC105373017 Neighboring gene RNA, U7 small nuclear 167 pseudogene Neighboring gene target of myb1 membrane trafficking protein Neighboring gene Sharpr-MPRA regulatory region 10159 Neighboring gene microRNA 3909

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?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
 
endosome to lysosome transport NAS
Non-traceable Author Statement
more info
PubMed 
negative regulation of Wnt signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
NURF complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
HMG domain-containing protein 4
Names
HMG box domain containing 4
HMG box-containing protein 4
high mobility group protein 2-like 1

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.

mRNA and Protein(s)

  1. NM_001003681.3NP_001003681.1  HMG domain-containing protein 4 isoform 1

    See identical proteins and their annotated locations for NP_001003681.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer protein (isoform 1).
    Source sequence(s)
    AI471703, BC040447, BC052624, DW452042
    Consensus CDS
    CCDS33641.1
    UniProtKB/Swiss-Prot
    Q9UGU5
    UniProtKB/TrEMBL
    Q7Z641
    Related
    ENSP00000216106.5, ENST00000216106.6
    Conserved Domains (2) summary
    cd00084
    Location:407470
    HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...
    pfam13775
    Location:107225
    DUF4171; Domain of unknown function (DUF4171)
  2. NM_001362972.2NP_001349901.1  HMG domain-containing protein 4 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks a 5' exon and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded protein (isoform 2) has a shorter N-terminus than isoform 1.
    Source sequence(s)
    AI471703, AL008635
    Conserved Domains (2) summary
    cd00084
    Location:298361
    HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...
    pfam13775
    Location:1123
    DUF4171; Domain of unknown function (DUF4171)

RNA

  1. NR_027780.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) includes an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI471703, AL079310, DW452042
    Related
    ENST00000418170.5

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p13 Primary Assembly

    Range
    35256697..35295807
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006724100.4XP_006724163.1  HMG domain-containing protein 4 isoform X1

    Conserved Domains (2) summary
    cd00084
    Location:450513
    HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...
    pfam13775
    Location:150268
    DUF4171; Domain of unknown function (DUF4171)
  2. XM_006724101.4XP_006724164.1  HMG domain-containing protein 4 isoform X2

    Conserved Domains (2) summary
    cd00084
    Location:450513
    HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...
    pfam13775
    Location:150268
    DUF4171; Domain of unknown function (DUF4171)
  3. XM_006724102.2XP_006724165.1  HMG domain-containing protein 4 isoform X3

    See identical proteins and their annotated locations for XP_006724165.1

    UniProtKB/Swiss-Prot
    Q9UGU5
    Conserved Domains (2) summary
    cd00084
    Location:298361
    HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...
    pfam13775
    Location:1123
    DUF4171; Domain of unknown function (DUF4171)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_005487.3: Suppressed sequence

    Description
    NM_005487.3: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
  2. NM_014250.1: Suppressed sequence

    Description
    NM_014250.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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