TXNL4A (thioredoxin like 4A)

Gene

• Entrez ID: 10907
• Gene name: Thioredoxin like 4A
• Gene symbol: TXNL4A
• Synonyms: BMKS, DIB1, DIM1, SNRNP15, TXNL4, U5-15kD
• Chromosome: 18
• Chromosome location: 18q23
• 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 int

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs535089924	CGCGCGCGCTAGCGCCGTGCGTGCTGACGGCATG>-,CGCGCGCGCTAGCGCCGTGCGTGCTGACGGCATGCGCGCGCGCTAGCGCCGTGCGTGCTGACGGCATG,CGCGCGCGCTAGCGCCGTGCGTGCTGACGGCATGCGCGCGCGCTAGCGCCGTGCGTGCTGACGGCATGCGCGCGCGCTAGCGCCGTGCGTGCTGACGGCATG	Pathogenic	Intron variant, upstream transcript variant, genic upstream transcript variant
rs727502793	C>A,T	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant, missense variant
rs727502794	G>A	Pathogenic	Stop gained, coding sequence variant, non coding transcript variant, intron variant, 5 prime UTR variant
rs727502795	A>-	Pathogenic	Coding sequence variant, non coding transcript variant, intron variant, splice donor variant, frameshift variant, 5 prime UTR variant
rs786205699	CGCGCTAGCGCCGTGCGTGCTGACGGCATGTGCG>-	Pathogenic	Genic upstream transcript variant, intron variant, upstream transcript variant
rs879255559	T>C	Pathogenic	Intron variant
rs1555719172	TAGGATCCCAGTCGTGGCCGAAG>-	Likely-pathogenic	5 prime UTR variant, non coding transcript variant, coding sequence variant, intron variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT052139	hsa-let-7b-5p	CLASH	23622248
MIRT050419	hsa-miR-23a-3p	CLASH	23622248
MIRT041224	hsa-miR-193b-3p	CLASH	23622248
MIRT036005	hsa-miR-1301-3p	CLASH	23622248
MIRT712648	hsa-miR-6752-3p	HITS-CLIP	19536157
MIRT712647	hsa-miR-3667-3p	HITS-CLIP	19536157
MIRT712646	hsa-miR-18a-3p	HITS-CLIP	19536157
MIRT712645	hsa-miR-938	HITS-CLIP	19536157
MIRT712644	hsa-miR-6886-3p	HITS-CLIP	19536157
MIRT712643	hsa-miR-670-3p	HITS-CLIP	19536157
MIRT712648	hsa-miR-6752-3p	HITS-CLIP	19536157
MIRT712647	hsa-miR-3667-3p	HITS-CLIP	19536157
MIRT712646	hsa-miR-18a-3p	HITS-CLIP	19536157
MIRT712645	hsa-miR-938	HITS-CLIP	19536157
MIRT712644	hsa-miR-6886-3p	HITS-CLIP	19536157
MIRT712643	hsa-miR-670-3p	HITS-CLIP	19536157
MIRT712648	hsa-miR-6752-3p	HITS-CLIP	19536157
MIRT712647	hsa-miR-3667-3p	HITS-CLIP	19536157
MIRT712646	hsa-miR-18a-3p	HITS-CLIP	19536157
MIRT712645	hsa-miR-938	HITS-CLIP	19536157
MIRT712644	hsa-miR-6886-3p	HITS-CLIP	19536157
MIRT712643	hsa-miR-670-3p	HITS-CLIP	19536157
MIRT712648	hsa-miR-6752-3p	HITS-CLIP	19536157
MIRT712647	hsa-miR-3667-3p	HITS-CLIP	19536157
MIRT712646	hsa-miR-18a-3p	HITS-CLIP	19536157
MIRT712645	hsa-miR-938	HITS-CLIP	19536157
MIRT712644	hsa-miR-6886-3p	HITS-CLIP	19536157
MIRT712643	hsa-miR-670-3p	HITS-CLIP	19536157
MIRT1465386	hsa-miR-1197	CLIP-seq
MIRT1465387	hsa-miR-125a-3p	CLIP-seq
MIRT1465388	hsa-miR-1273f	CLIP-seq
MIRT1465389	hsa-miR-3180	CLIP-seq
MIRT1465390	hsa-miR-3180-3p	CLIP-seq
MIRT1465391	hsa-miR-3196	CLIP-seq
MIRT1465392	hsa-miR-329	CLIP-seq
MIRT1465393	hsa-miR-362-3p	CLIP-seq
MIRT1465394	hsa-miR-3647-3p	CLIP-seq
MIRT1465395	hsa-miR-3675-5p	CLIP-seq
MIRT1465396	hsa-miR-3714	CLIP-seq
MIRT1465397	hsa-miR-4493	CLIP-seq
MIRT1465398	hsa-miR-4756-3p	CLIP-seq
MIRT1465399	hsa-miR-552	CLIP-seq
MIRT2360593	hsa-miR-3121-3p	CLIP-seq
MIRT2360594	hsa-miR-320a	CLIP-seq
MIRT2360595	hsa-miR-320b	CLIP-seq
MIRT2360596	hsa-miR-320c	CLIP-seq
MIRT2360597	hsa-miR-320d	CLIP-seq
MIRT2360598	hsa-miR-361-3p	CLIP-seq
MIRT2360599	hsa-miR-3907	CLIP-seq
MIRT2360600	hsa-miR-4429	CLIP-seq
MIRT2360601	hsa-miR-4677-3p	CLIP-seq
MIRT2360602	hsa-miR-4742-3p	CLIP-seq
MIRT2360603	hsa-miR-518a-5p	CLIP-seq
MIRT2360604	hsa-miR-527	CLIP-seq
MIRT2360605	hsa-miR-664	CLIP-seq
MIRT2360606	hsa-miR-766	CLIP-seq
MIRT2360598	hsa-miR-361-3p	CLIP-seq
MIRT2462695	hsa-miR-4786-3p	CLIP-seq
MIRT2360593	hsa-miR-3121-3p	CLIP-seq
MIRT2360602	hsa-miR-4742-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000245	Process	Spliceosomal complex assembly	TAS	10610776
GO:0000375	Process	RNA splicing, via transesterification reactions	TAS	10610776
GO:0000398	Process	MRNA splicing, via spliceosome	IDA	28781166
GO:0000398	Process	MRNA splicing, via spliceosome	TAS
GO:0005515	Function	Protein binding	IPI	15840814, 20858735, 25416956, 28514442, 32296183
GO:0005634	Component	Nucleus	IDA	26912367
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005681	Component	Spliceosomal complex	IBA	21873635
GO:0005681	Component	Spliceosomal complex	TAS	10610776
GO:0005682	Component	U5 snRNP	IBA	21873635
GO:0005829	Component	Cytosol	IDA
GO:0007049	Process	Cell cycle	IEA
GO:0031965	Component	Nuclear membrane	IDA
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IBA	21873635
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IDA	26912367
GO:0051301	Process	Cell division	IEA
GO:0071005	Component	U2-type precatalytic spliceosome	IDA	28781166

Other IDs

• MIM: 611595
• HGNC: 30551
• e!Ensembl: ENSG00000141759

Protein

• UniProt ID: P83876
• Protein name: Thioredoxin-like protein 4A (DIM1 protein homolog) (Spliceosomal U5 snRNP-specific 15 kDa protein) (Thioredoxin-like U5 snRNP protein U5-15kD)
• Protein function: Plays a role in pre-mRNA splicing as component of the U5 snRNP and U4/U6-U5 tri-snRNP complexes that are involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex). {ECO:0000269|PubMed:28781166, EC
• PDB: 1PQN, 1QGV, 1SYX, 3JCR, 4BWQ, 4BWS, 4CDO, 5O9Z, 6AH0, 6AHD, 6QW6, 6QX9, 8H6E, 8H6J, 8H6K, 8H6L, 8Q7N, 8QO9, 8QOZ, 8QP8, 8QP9, 8QPA, 8QPB, 8QPE, 8QPK, 8QXD, 8QZS, 8R08, 8R09, 8R0A, 8R0B, 8RM5
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF02966	DIM1	4 → 136	Mitosis protein DIM1	Domain

• Sequence:

  MSYMLPHLHNGWQVDQAILSEEDRVVVIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYL
  VDITEVPDFNKMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINWAMEDKQEMVDIIETVY
  RGARKGRGLVVSPKDYSTKYRY

• Sequence length: 142

Pathways

KEGG:

Spliceosome

Reactome:

mRNA Splicing - Major Pathway
mRNA Splicing - Minor Pathway

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Atrial septal defect	Atrial Septal Defects	rs137852951, rs137852953, rs137852955, rs267607106, rs104893900, rs104893901, rs104893903, rs606231358, rs606231359, rs137852683, rs606231360, rs104893907, rs104894073, rs1585703301, rs104894074, rs267606903, rs121912677, rs387906585, rs387906773, rs72554028, rs587782928, rs587782929, rs587782930, rs587784067, rs1555226315, rs879253754, rs1114167356, rs773922431, rs1554093487, rs1554093433, rs1554093461, rs1561621507, rs1561619801, rs766692577, rs1581108237, rs1581111034, rs1579663872, rs1583066622, rs1456289029, rs1761430125
Hearing loss	Conductive hearing loss	rs267607135, rs267606855, rs779841884, rs267606854, rs28942097, rs121908073, rs121908076, rs74315289, rs121908144, rs111033313, rs74315437, rs121908348, rs121908349, rs121908350, rs397515359, rs180177151, rs180177154, rs180177153, rs35689081, rs35887622, rs80338944, rs104894396, rs104894398, rs80338947, rs80338948, rs80338942, rs104894402, rs104894403, rs80338945, rs28931594, rs80338940, rs80338941, rs80356590, rs80338950, rs387906706, rs387906707, rs387906708, rs398122848, rs387907016, rs587776894, rs387907088, rs397515411, rs370965183, rs398122930, rs199897298, rs111033187, rs111033448, rs199606180, rs111033284, rs397516413, rs111033305, rs111033220, rs111033256, rs111033297, rs111033253, rs104894408, rs111033295, rs397516874, rs76434661, rs111033335, rs397517323, rs111033247, rs367928692, rs374793617, rs143939430, rs397515605, rs80338939, rs200656442, rs779748859, rs587781261, rs587781262, rs143343083, rs200147906, rs730880338, rs797044491, rs146281367, rs756484720, rs869025593, rs201306709, rs540895576, rs777777359, rs879255246, rs1554358720, rs142498437, rs377145777, rs1057517519, rs779077039, rs952741388, rs1060499797, rs764139009, rs1060499590, rs1064794012, rs1064797115, rs756790858, rs775633137, rs1554952443, rs1554952193, rs782063761, rs1199012623, rs756147087, rs1555648043, rs1555661490, rs1553196233, rs781546107, rs111033190, rs775428246, rs782539587, rs537227442, rs148695069, rs1554835827, rs953422571, rs1554834186, rs1554834161, rs1554835103, rs1554577339, rs1554577402, rs768471577, rs782279338, rs781951909, rs998045226, rs375759781, rs755804651, rs1557458426, rs767797828, rs538027448, rs1559366084, rs367688416, rs1558480402, rs1558490542, rs1559870857, rs1560690591, rs1561299289, rs1562817224, rs1562817529, rs1562822565, rs1562835391, rs1564113368, rs1564554255, rs773851192, rs1564555240, rs761261855, rs1564805114, rs1565522273, rs1565127413, rs781790246, rs1565430886, rs1565469959, rs746667217, rs1565819402, rs1565855932, rs150529554, rs1567939793, rs201866631, rs754472294, rs1559372512, rs1558464965, rs1558488902, rs775062249, rs1226171550, rs1561590396, rs765574676, rs762876554, rs757327146, rs1564949059, rs1565519673, rs368050948, rs1565541888, rs781989117, rs1565402473, rs750358148, rs1386887007, rs1209665716, rs1567641234, rs1237955948, rs1569042782, rs752672077, rs146689036, rs1560070780, rs149712664, rs1564556995, rs762226905, rs773573968, rs1568528171, rs1198256157, rs377267777, rs370564476, rs1577876794, rs747787770, rs759432278, rs1043716893, rs1581138934, rs2033773650, rs1421964916, rs771766431, rs780917129, rs1895773215, rs1895769400, rs761543680, rs1565920060
Ventricular septal defect	Ventricular Septal Defects	rs104894073, rs387906775

Unknown
Disease name	Disease term	dbSNP ID	References
Blepharophimosis	Blepharophimosis
Burn-mckeown syndrome	Burn-Mckeown syndrome		25434003
Choanal atresia	Bilateral choanal atresia/stenosis
Dwarfism	Dwarfism
Heart septal defects	Heart Septal Defects
Malocclusion	Class III malocclusion
Micrognathism	Micrognathism
Microstomia	Microstomia
Renal hypoplasia	Congenital hypoplasia of kidney	rs561111097
Syndactyly of the toes	2-3 toe syndactyly