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TXNL4A thioredoxin like 4A [ Homo sapiens (human) ]

Gene ID: 10907, updated on 7-Jan-2019

Summary

Official Symbol
TXNL4Aprovided by HGNC
Official Full Name
thioredoxin like 4Aprovided by HGNC
Primary source
HGNC:HGNC:30551
See related
Ensembl:ENSG00000141759 MIM:611595
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
BMKS; DIB1; DIM1; TXNL4; SNRNP15; U5-15kD
Summary
The protein encoded by this gene is a member of the U5 small ribonucleoprotein particle (snRNP), and is involved in pre-mRNA splicing. This protein contains a thioredoxin-like fold and it is expected to interact with multiple proteins. Protein-protein interactions have been observed with the polyglutamine tract-binding protein 1 (PQBP1). Mutations in both the coding region and promoter region of this gene have been associated with Burn-McKeown syndrome, which is a rare disorder characterized by craniofacial dysmorphisms, cardiac defects, hearing loss, and bilateral choanal atresia. A pseudogene of this gene is found on chromosome 2. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2015]
Expression
Ubiquitous expression in brain (RPKM 13.4), testis (RPKM 11.6) and 25 other tissues See more
Orthologs

Genomic context

See TXNL4A in Genome Data Viewer
Location:
18q23
Exon count:
7
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 18 NC_000018.10 (79972867..80033935, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (77732867..77748546, complement)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene potassium voltage-gated channel modifier subfamily G member 2 Neighboring gene PQ loop repeat containing 1 Neighboring gene heat shock factor binding protein 1 like 1 Neighboring gene ribosome binding factor A Neighboring gene solute carrier family 25 member 6 pseudogene 4 Neighboring gene RBFA downstream neighbor

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 FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • Spliceosome, organism-specific biosystem (from KEGG)
    Spliceosome, organism-specific biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, conserved biosystem (from KEGG)
    Spliceosome, conserved biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, U4/U6.U5 tri-snRNP, organism-specific biosystem (from KEGG)
    Spliceosome, U4/U6.U5 tri-snRNP, organism-specific biosystemStructural complex; Genetic information processing; Spliceosome
  • Spliceosome, U4/U6.U5 tri-snRNP, conserved biosystem (from KEGG)
    Spliceosome, U4/U6.U5 tri-snRNP, conserved biosystemStructural complex; Genetic information processing; Spliceosome
  • mRNA Processing, organism-specific biosystem (from WikiPathways)
    mRNA Processing, organism-specific biosystemThis process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' po...
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...
  • mRNA Splicing - Minor Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Minor Pathway, organism-specific biosystemThe splicing of a subset of pre-mRNA introns occurs by a second pathway, designated the AT-AC or U12-dependent splicing pathway. AT-AC introns have highly conserved, non-canonical splice sites that ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
RNA splicing, via transesterification reactions TAS
Traceable Author Statement
more info
PubMed 
cell cycle IEA
Inferred from Electronic Annotation
more info
 
cell division IEA
Inferred from Electronic Annotation
more info
 
mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
spliceosomal complex assembly TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
U2-type precatalytic spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
U4/U6 x U5 tri-snRNP complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U4/U6 x U5 tri-snRNP complex IDA
Inferred from Direct Assay
more info
PubMed 
U5 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
nuclear membrane IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
spliceosomal complex TAS
Traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
thioredoxin-like protein 4A
Names
DIM1 protein homolog
spliceosomal U5 snRNP-specific 15 kDa protein
thioredoxin-like 4
thioredoxin-like U5 snRNP protein U5-15kD

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.

Genomic

  1. NG_042061.1 RefSeqGene

    Range
    5001..66069
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001303471.2NP_001290400.1  thioredoxin-like protein 4A isoform 2

    See identical proteins and their annotated locations for NP_001290400.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate exon in its 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AK309098, BC001046, BE385528, BF972457
    UniProtKB/Swiss-Prot
    P83876
    Conserved Domains (1) summary
    cl00388
    Location:13103
    Thioredoxin_like; Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold
  2. NM_001305557.1NP_001292486.1  thioredoxin-like protein 4A isoform 3

    See identical proteins and their annotated locations for NP_001292486.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1, but has the same N- and C-termini.
    Source sequence(s)
    BC001046, BE385528, BF972457, BM922767
    UniProtKB/Swiss-Prot
    P83876
    Conserved Domains (1) summary
    PLN00410
    Location:1134
    PLN00410; U5 snRNP protein, DIM1 family; Provisional
  3. NM_001305563.1NP_001292492.1  thioredoxin-like protein 4A isoform 4

    See identical proteins and their annotated locations for NP_001292492.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains two alternate exons in its 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus than isoform 1. Variants 4 and 5 encode the same isoform (4).
    Source sequence(s)
    AC090360, AV729855, BC001046, BQ011103
    Consensus CDS
    CCDS82260.1
    UniProtKB/Swiss-Prot
    P83876
    UniProtKB/TrEMBL
    K7ESL1
    Related
    ENSP00000465493.1, ENST00000592957.1
    Conserved Domains (1) summary
    cl00388
    Location:171
    Thioredoxin_like; Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold
  4. NM_001305564.1NP_001292493.1  thioredoxin-like protein 4A isoform 4

    See identical proteins and their annotated locations for NP_001292493.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) contains an alternate exon in its 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus than isoform 1. Variants 4 and 5 encode the same isoform (4).
    Source sequence(s)
    AV729855, BC001046, BQ011103
    Consensus CDS
    CCDS82260.1
    UniProtKB/Swiss-Prot
    P83876
    UniProtKB/TrEMBL
    K7ESL1
    Related
    ENSP00000465572.1, ENST00000585474.5
    Conserved Domains (1) summary
    cl00388
    Location:171
    Thioredoxin_like; Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold
  5. NM_006701.5NP_006692.1  thioredoxin-like protein 4A isoform 1

    See identical proteins and their annotated locations for NP_006692.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC090360, BC001046, BE385528, BF972457
    Consensus CDS
    CCDS32852.1
    UniProtKB/Swiss-Prot
    P83876
    Related
    ENSP00000269601.4, ENST00000269601.9
    Conserved Domains (1) summary
    PLN00410
    Location:1142
    PLN00410; U5 snRNP protein, DIM1 family; Provisional

RNA

  1. NR_131175.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) contains two alternate internal exons, 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)
    AA923682, AK309098, AL522879, BC001046, BE385528, BF972457
  2. NR_131176.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) contains an alternate internal 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)
    AA923682, BC001046, BE385528, BF972457, BU553165
  3. NR_131177.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AW796546, BC001046, BE385528, BF972457

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000018.10 Reference GRCh38.p12 Primary Assembly

    Range
    79972867..80033935 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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