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

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; AllianceGenome:HGNC:30551
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: mouse all
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Genomic context

Location:: 18q23

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	18	NC_000018.10 (79970813..80033936, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	18	NC_060942.1 (80247334..80310473, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	18	NC_000018.9 (77730813..77793936, complement)

Chromosome 18 - NC_000018.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Expanding the genotypic spectrum of TXNL4A variants in Burn-McKeown syndrome.
Title: Expanding the genotypic spectrum of TXNL4A variants in Burn-McKeown syndrome.
Burn-McKeown syndrome with biallelic promoter type 2 deletion in TXNL4A in two siblings.
Title: Burn-McKeown syndrome with biallelic promoter type 2 deletion in TXNL4A in two siblings.
The Renpenning syndrome-associated protein PQBP1 facilitates the nuclear import of splicing factor TXNL4A through the karyopherin beta2 receptor.
Title: The Renpenning syndrome-associated protein PQBP1 facilitates the nuclear import of splicing factor TXNL4A through the karyopherin β2 receptor.
Recessive variants in TXNL4A were identified in two individuals with Burn-McKeown syndrome as well as in three individuals (from two families) with isolated choanal atresia.
Title: Identification of causative variants in TXNL4A in Burn-McKeown syndrome and isolated choanal atresia.
results suggest that the interaction between PQBP1 and WBP11 negatively modulates the U5-15kD binding of PQBP1 by an allosteric mechanism
Title: Allosteric modulation of the binding affinity between PQBP1 and the spliceosomal protein U5-15kD.
Reporter gene and in vivo assays showed that the promoter deletions led to reduced expression of TXNL4A. Depletion of TXNL4A (Dib1) in yeast demonstrated reduced assembly of the tri-snRNP complex.
Title: Compound heterozygosity of low-frequency promoter deletions and rare loss-of-function mutations in TXNL4A causes Burn-McKeown syndrome.
frameshift mutations in the PQBP-1 gene lead to expression of mutants lacking the ability to interact with U5-15kD
Title: Polyglutamine tract-binding protein-1 binds to U5-15kD via a continuous 23-residue segment of the C-terminal domain.
human dim1 is a peptidase with autocleavage activity that results in a thioredoxin-like core
Title: Identification of human dim1 as a peptidase with autocleavage activity.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Choanal atresia-hearing loss-cardiac defects-craniofacial dysmorphism syndrome MedGen: C1837822 OMIM: 608572 GeneReviews: TXNL4A-Related Craniofacial Disorders	Compare labs

Variation

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See variants in ClinVar

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

RH1664 (e-PCR)
- UniSTS:85122

D18S553 (e-PCR)
- UniSTS:148688

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA splicing, via transesterification reactions	TAS Traceable Author Statement more info	PubMed
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in mRNA splicing, via spliceosome	IDA Inferred from Direct Assay more info	PubMed
involved_in mRNA splicing, via spliceosome	NAS Non-traceable Author Statement more info	PubMed
involved_in spliceosomal complex assembly	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of U2-type precatalytic spliceosome	IDA Inferred from Direct Assay more info	PubMed
part_of U4/U6 x U5 tri-snRNP complex	IBA Inferred from Biological aspect of Ancestor more info
part_of U4/U6 x U5 tri-snRNP complex	IDA Inferred from Direct Assay more info	PubMed
part_of U4/U6 x U5 tri-snRNP complex	IPI Inferred from Physical Interaction more info	PubMed
part_of U5 snRNP	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed
part_of spliceosomal complex	IBA Inferred from Biological aspect of Ancestor more info
part_of spliceosomal complex	TAS Traceable Author Statement more info	PubMed

General protein information

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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)

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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.

Genomic

NG_042061.2 RefSeqGene

Range

50373..68123

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001303471.3 → NP_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)

AC090360, AK309098, BC001046, BE385528, BF972457

UniProtKB/Swiss-Prot

P83876

Conserved Domains (1) summary

cl00388
Location:13 → 103

Thioredoxin_like; Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold
NM_001305557.2 → NP_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)

AC090360, BC001046, BE385528, BF972457, BM922767

UniProtKB/Swiss-Prot

P83876

Conserved Domains (1) summary

PLN00410
Location:1 → 134

PLN00410; U5 snRNP protein, DIM1 family; Provisional
NM_001305563.2 → NP_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/TrEMBL

K7ESL1

Related

ENSP00000465493.1, ENST00000592957.1

Conserved Domains (1) summary

cl00388
Location:1 → 71

Thioredoxin_like; Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold
NM_001305564.2 → NP_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)

AC090360, AV729855, BC001046, BQ011103

Consensus CDS

CCDS82260.1

UniProtKB/TrEMBL

K7ESL1

Related

ENSP00000465572.1, ENST00000585474.5

Conserved Domains (1) summary

cl00388
Location:1 → 71

Thioredoxin_like; Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold
NM_006701.5 → NP_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

B2RC18, O14834, P83876

Related

ENSP00000269601.4, ENST00000269601.10

Conserved Domains (1) summary

PLN00410
Location:1 → 142

PLN00410; U5 snRNP protein, DIM1 family; Provisional

RNA

NR_131175.2 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, AC090360, AK309098, AL522879, BC001046, BE385528, BF972457
NR_131176.2 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, AC090360, BC001046, BE385528, BF972457, BU553165
NR_131177.2 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)

AC090360, AW796546, BC001046, BE385528, BF972457