Human Gene TXNL4A (ENST00000269601.10_7) from GENCODE V47lift37
  Description: thioredoxin like 4A, transcript variant 1 (from RefSeq NM_006701.5)
Gencode Transcript: ENST00000269601.10_7
Gencode Gene: ENSG00000141759.15_9
Transcript (Including UTRs)
   Position: hg19 chr18:77,730,813-77,748,563 Size: 17,751 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr18:77,733,685-77,748,392 Size: 14,708 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr18:77,730,813-77,748,563)mRNA (may differ from genome)Protein (142 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TXN4A_HUMAN
DESCRIPTION: RecName: Full=Thioredoxin-like protein 4A; AltName: Full=DIM1 protein homolog; AltName: Full=Spliceosomal U5 snRNP-specific 15 kDa protein; AltName: Full=Thioredoxin-like U5 snRNP protein U5-15kD;
FUNCTION: Essential role in pre-mRNA splicing.
SUBUNIT: Interacts with HNRPF, HNRPH2, NEDD9, ERBB4, and PQBP1.
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Belongs to the DIM1 family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: TXNL4A
Diseases sorted by gene-association score: burn-mckeown syndrome* (940), choanal atresia-hearing loss-cardiac defects-craniofacial dysmorphism syndrome* (400), acrofacial dysostosis 1, nager type (8), choanal atresia, posterior (8), acrofacial dysostosis (6), treacher collins syndrome 1 (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 23.26 RPKM in Testis
Total median expression: 589.03 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -100.90171-0.590 Picture PostScript Text
3' UTR -943.202872-0.328 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR004123 - mRNA_splic_U5
IPR012336 - Thioredoxin-like_fold

Pfam Domains:
PF00085 - Thioredoxin
PF02966 - Mitosis protein DIM1

SCOP Domains:
52833 - Thioredoxin-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1PQN - NMR MuPIT 1QGV - X-ray MuPIT 1SYX - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P83876
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0000245 spliceosomal complex assembly
GO:0000375 RNA splicing, via transesterification reactions
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0007049 cell cycle
GO:0008380 RNA splicing
GO:0051301 cell division

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005682 U5 snRNP
GO:0005829 cytosol
GO:0031965 nuclear membrane
GO:0046540 U4/U6 x U5 tri-snRNP complex


-  Descriptions from all associated GenBank mRNAs
  JD517575 - Sequence 498599 from Patent EP1572962.
JD366429 - Sequence 347453 from Patent EP1572962.
JD155864 - Sequence 136888 from Patent EP1572962.
JD335653 - Sequence 316677 from Patent EP1572962.
JD443130 - Sequence 424154 from Patent EP1572962.
JD025443 - Sequence 6467 from Patent EP1572962.
JD035216 - Sequence 16240 from Patent EP1572962.
JD283327 - Sequence 264351 from Patent EP1572962.
JD112315 - Sequence 93339 from Patent EP1572962.
JD425592 - Sequence 406616 from Patent EP1572962.
JD475799 - Sequence 456823 from Patent EP1572962.
JD277914 - Sequence 258938 from Patent EP1572962.
BC001046 - Homo sapiens thioredoxin-like 4A, mRNA (cDNA clone MGC:1296 IMAGE:2823293), complete cds.
BC019272 - Homo sapiens thioredoxin-like 4A, mRNA (cDNA clone MGC:3529 IMAGE:2823293), complete cds.
AK308703 - Homo sapiens cDNA, FLJ98744.
JD490111 - Sequence 471135 from Patent EP1572962.
JD092778 - Sequence 73802 from Patent EP1572962.
JD433207 - Sequence 414231 from Patent EP1572962.
JD232552 - Sequence 213576 from Patent EP1572962.
JD206598 - Sequence 187622 from Patent EP1572962.
JD486019 - Sequence 467043 from Patent EP1572962.
JD564947 - Sequence 545971 from Patent EP1572962.
JD073245 - Sequence 54269 from Patent EP1572962.
AK309098 - Homo sapiens cDNA, FLJ99139.
JD316915 - Sequence 297939 from Patent EP1572962.
JD129393 - Sequence 110417 from Patent EP1572962.
AF023611 - Homo sapiens Dim1p homolog (hdim1+) mRNA, complete cds.
AF023612 - Homo sapiens Dim1p homolog mRNA, complete cds.
JD309542 - Sequence 290566 from Patent EP1572962.
JD108835 - Sequence 89859 from Patent EP1572962.
JD372534 - Sequence 353558 from Patent EP1572962.
JD224490 - Sequence 205514 from Patent EP1572962.
AF146373 - Homo sapiens thioredoxin-like U5 snRNP protein U5-15kD mRNA, complete cds.
AK314901 - Homo sapiens cDNA, FLJ95806, Homo sapiens thioredoxin-like 4 (TXNL4), mRNA.
JF432486 - Synthetic construct Homo sapiens clone IMAGE:100073707 thioredoxin-like 4A (TXNL4A) gene, encodes complete protein.
KJ893161 - Synthetic construct Homo sapiens clone ccsbBroadEn_02555 TXNL4A gene, encodes complete protein.
AB528659 - Synthetic construct DNA, clone: pF1KB6740, Homo sapiens TXNL4A gene for thioredoxin-like protein 4A, without stop codon, in Flexi system.
JD294452 - Sequence 275476 from Patent EP1572962.
JD456665 - Sequence 437689 from Patent EP1572962.
JD484757 - Sequence 465781 from Patent EP1572962.
JD408990 - Sequence 390014 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P83876 (Reactome details) participates in the following event(s):

R-HSA-75083 ATAC spliceosome mediated 3' splice site cleavage, exon ligation
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-75081 Formation of AT-AC B Complex
R-HSA-75082 ATAC spliceosome mediated Lariat formation,5' splice site cleavage
R-HSA-75079 Formation of AT-AC C complex
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72165 mRNA Splicing - Minor Pathway
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: B2RC18, DIM1, ENST00000269601.1, ENST00000269601.2, ENST00000269601.3, ENST00000269601.4, ENST00000269601.5, ENST00000269601.6, ENST00000269601.7, ENST00000269601.8, ENST00000269601.9, NM_006701, O14834, P83876, TXN4A_HUMAN, TXNL4, uc317ise.1, uc317ise.2
UCSC ID: ENST00000269601.10_7
RefSeq Accession: NM_006701.5
Protein: P83876 (aka TXN4A_HUMAN or TX4A_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene TXNL4A:
burn-mckeown (TXNL4A-Related Craniofacial Disorders)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.