LOCUS       NM_006701               3472 bp    mRNA    linear   PRI 08-OCT-2024
DEFINITION  Homo sapiens thioredoxin like 4A (TXNL4A), transcript variant 1,
            mRNA.
ACCESSION   NM_006701 XM_351169
VERSION     NM_006701.5
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 3472)
  AUTHORS   Cho,N.H., Cheveralls,K.C., Brunner,A.D., Kim,K., Michaelis,A.C.,
            Raghavan,P., Kobayashi,H., Savy,L., Li,J.Y., Canaj,H., Kim,J.Y.S.,
            Stewart,E.M., Gnann,C., McCarthy,F., Cabrera,J.P., Brunetti,R.M.,
            Chhun,B.B., Dingle,G., Hein,M.Y., Huang,B., Mehta,S.B.,
            Weissman,J.S., Gomez-Sjoberg,R., Itzhak,D.N., Royer,L.A., Mann,M.
            and Leonetti,M.D.
  TITLE     OpenCell: Endogenous tagging for the cartography of human cellular
            organization
  JOURNAL   Science 375 (6585), eabi6983 (2022)
   PUBMED   35271311
REFERENCE   2  (bases 1 to 3472)
  AUTHORS   Wood,K.A., Ellingford,J.M., Thomas,H.B., Douzgou,S., Beaman,G.M.,
            Hobson,E., Prescott,K., O'Keefe,R.T. and Newman,W.G.
  CONSRTM   Genomics UK Research Consortium
  TITLE     Expanding the genotypic spectrum of TXNL4A variants in Burn-McKeown
            syndrome
  JOURNAL   Clin Genet 101 (2), 255-259 (2022)
   PUBMED   34713892
  REMARK    GeneRIF: Expanding the genotypic spectrum of TXNL4A variants in
            Burn-McKeown syndrome.
REFERENCE   3  (bases 1 to 3472)
  AUTHORS   Huttlin,E.L., Bruckner,R.J., Navarrete-Perea,J., Cannon,J.R.,
            Baltier,K., Gebreab,F., Gygi,M.P., Thornock,A., Zarraga,G., Tam,S.,
            Szpyt,J., Gassaway,B.M., Panov,A., Parzen,H., Fu,S., Golbazi,A.,
            Maenpaa,E., Stricker,K., Guha Thakurta,S., Zhang,T., Rad,R.,
            Pan,J., Nusinow,D.P., Paulo,J.A., Schweppe,D.K., Vaites,L.P.,
            Harper,J.W. and Gygi,S.P.
  TITLE     Dual proteome-scale networks reveal cell-specific remodeling of the
            human interactome
  JOURNAL   Cell 184 (11), 3022-3040 (2021)
   PUBMED   33961781
REFERENCE   4  (bases 1 to 3472)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   5  (bases 1 to 3472)
  AUTHORS   Wieczorek,D., Newman,W.G., Wieland,T., Berulava,T., Kaffe,M.,
            Falkenstein,D., Beetz,C., Graf,E., Schwarzmayr,T., Douzgou,S.,
            Clayton-Smith,J., Daly,S.B., Williams,S.G., Bhaskar,S.S.,
            Urquhart,J.E., Anderson,B., O'Sullivan,J., Boute,O., Gundlach,J.,
            Czeschik,J.C., van Essen,A.J., Hazan,F., Park,S., Hing,A.,
            Kuechler,A., Lohmann,D.R., Ludwig,K.U., Mangold,E., Steenpass,L.,
            Zeschnigk,M., Lemke,J.R., Lourenco,C.M., Hehr,U., Prott,E.C.,
            Waldenberger,M., Bohmer,A.C., Horsthemke,B., O'Keefe,R.T.,
            Meitinger,T., Burn,J., Ludecke,H.J. and Strom,T.M.
  TITLE     Compound heterozygosity of low-frequency promoter deletions and
            rare loss-of-function mutations in TXNL4A causes Burn-McKeown
            syndrome
  JOURNAL   Am J Hum Genet 95 (6), 698-707 (2014)
   PUBMED   25434003
  REMARK    GeneRIF: 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.
REFERENCE   6  (bases 1 to 3472)
  AUTHORS   Zhou,Z., Licklider,L.J., Gygi,S.P. and Reed,R.
  TITLE     Comprehensive proteomic analysis of the human spliceosome
  JOURNAL   Nature 419 (6903), 182-185 (2002)
   PUBMED   12226669
REFERENCE   7  (bases 1 to 3472)
  AUTHORS   Zhang,Y., Lindblom,T., Chang,A., Sudol,M., Sluder,A.E. and
            Golemis,E.A.
  TITLE     Evidence that dim1 associates with proteins involved in pre-mRNA
            splicing, and delineation of residues essential for dim1
            interactions with hnRNP F and Npw38/PQBP-1
  JOURNAL   Gene 257 (1), 33-43 (2000)
   PUBMED   11054566
REFERENCE   8  (bases 1 to 3472)
  AUTHORS   Reuter,K., Nottrott,S., Fabrizio,P., Luhrmann,R. and Ficner,R.
  TITLE     Identification, characterization and crystal structure analysis of
            the human spliceosomal U5 snRNP-specific 15 kD protein
  JOURNAL   J Mol Biol 294 (2), 515-525 (1999)
   PUBMED   10610776
REFERENCE   9  (bases 1 to 3472)
  AUTHORS   Zhang,Y.Z., Gould,K.L., Dunbrack,R.L. Jr., Cheng,H., Roder,H. and
            Golemis,E.A.
  TITLE     The evolutionarily conserved Dim1 protein defines a novel branch of
            the thioredoxin fold superfamily
  JOURNAL   Physiol Genomics 1 (3), 109-118 (1999)
   PUBMED   11015569
  REMARK    Publication Status: Online-Only
REFERENCE   10 (bases 1 to 3472)
  AUTHORS   Ludecke,H.J. and Wieczorek,D.
  TITLE     TXNL4A-Related Craniofacial Disorders
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   27413799
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BF972457.1, BE385528.1,
            BC001046.2 and AC090360.9.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_006701.4.
            
            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].
            
            Transcript Variant: This variant (1) encodes the longest isoform
            (1).
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1163658.399717.1,
                                           SRR1803614.279453.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000269601.10/ ENSP00000269601.4
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-38                BF972457.1         31-68
            39-675              BE385528.1         4-640
            676-1418            BC001046.2         645-1387
            1419-3472           AC090360.9         32741-34794         c
FEATURES             Location/Qualifiers
     source          1..3472
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="18"
                     /map="18q23"
     gene            1..3472
                     /gene="TXNL4A"
                     /gene_synonym="BMKS; DIB1; DIM1; SNRNP15; TXNL4; U5-15kD"
                     /note="thioredoxin like 4A"
                     /db_xref="GeneID:10907"
                     /db_xref="HGNC:HGNC:30551"
                     /db_xref="MIM:611595"
     exon            1..324
                     /gene="TXNL4A"
                     /gene_synonym="BMKS; DIB1; DIM1; SNRNP15; TXNL4; U5-15kD"
                     /inference="alignment:Splign:2.1.0"
     CDS             172..600
                     /gene="TXNL4A"
                     /gene_synonym="BMKS; DIB1; DIM1; SNRNP15; TXNL4; U5-15kD"
                     /note="isoform 1 is encoded by transcript variant 1;
                     thioredoxin-like 4; DIM1 protein homolog; thioredoxin-like
                     U5 snRNP protein U5-15kD; spliceosomal U5 snRNP-specific
                     15 kDa protein"
                     /codon_start=1
                     /product="thioredoxin-like protein 4A isoform 1"
                     /protein_id="NP_006692.1"
                     /db_xref="CCDS:CCDS32852.1"
                     /db_xref="GeneID:10907"
                     /db_xref="HGNC:HGNC:30551"
                     /db_xref="MIM:611595"
                     /translation="MSYMLPHLHNGWQVDQAILSEEDRVVVIRFGHDWDPTCMKMDEV
                     LYSIAEKVKNFAVIYLVDITEVPDFNKMYELYDPCTVMFFFRNKHIMIDLGTGNNNKI
                     NWAMEDKQEMVDIIETVYRGARKGRGLVVSPKDYSTKYRY"
     exon            325..428
                     /gene="TXNL4A"
                     /gene_synonym="BMKS; DIB1; DIM1; SNRNP15; TXNL4; U5-15kD"
                     /inference="alignment:Splign:2.1.0"
     exon            429..3472
                     /gene="TXNL4A"
                     /gene_synonym="BMKS; DIB1; DIM1; SNRNP15; TXNL4; U5-15kD"
                     /inference="alignment:Splign:2.1.0"
     regulatory      748..753
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TXNL4A"
                     /gene_synonym="BMKS; DIB1; DIM1; SNRNP15; TXNL4; U5-15kD"
                     /note="hexamer: AATAAA"
     polyA_site      772
                     /gene="TXNL4A"
                     /gene_synonym="BMKS; DIB1; DIM1; SNRNP15; TXNL4; U5-15kD"
                     /note="major polyA site"
     regulatory      853..858
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TXNL4A"
                     /gene_synonym="BMKS; DIB1; DIM1; SNRNP15; TXNL4; U5-15kD"
                     /note="hexamer: AGTAAA"
     polyA_site      879
                     /gene="TXNL4A"
                     /gene_synonym="BMKS; DIB1; DIM1; SNRNP15; TXNL4; U5-15kD"
     regulatory      3458..3463
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TXNL4A"
                     /gene_synonym="BMKS; DIB1; DIM1; SNRNP15; TXNL4; U5-15kD"
                     /note="hexamer: AATAAT"
     polyA_site      3472
                     /gene="TXNL4A"
                     /gene_synonym="BMKS; DIB1; DIM1; SNRNP15; TXNL4; U5-15kD"
ORIGIN      
        1 agacgttctg ccgggtggca gtcccagcgg agtttgcgtg tgcgggcggg accggatttc
       61 gtccgtgggc ccgggggcgg cgggggccgg ggagtgaggg gccggctgag cccacctcgc
      121 tgggccctcc ctggcgcccc gccttgggcg gcggcgagcg cgcgggccgc catgtcgtac
      181 atgctcccgc acctgcacaa cggctggcag gtggaccagg ccatcctctc ggaggaggac
      241 cgcgtggtcg tcatccgctt cggccacgac tgggatccta cgtgcatgaa gatggacgag
      301 gtcctgtaca gcatcgccga gaaggttaaa aattttgcag ttatttatct tgtggatatt
      361 acagaagtgc ctgacttcaa caaaatgtat gagttatacg atccatgtac tgtcatgttt
      421 ttcttcagga acaagcacat catgattgac ttggggactg gcaacaacaa caagattaac
      481 tgggccatgg aggacaagca ggagatggtg gacatcatcg agacggtgta ccgcggggcc
      541 cgcaaaggcc gcggcctggt ggtgtccccc aaggactact ccaccaagta ccgctactga
      601 ggcgccctca gtctgcgcgg ataaatgtcg tggagccctt tttgtatgga aacgttttaa
      661 gctatttaaa gcctttggaa aatacaggaa gctccagggc tggagcacct ctgagatgga
      721 attgataaca tggtcttaac tcaccgaaat aaacaagcac gtggtgagag gagcaggcct
      781 acttgtttgt tctcaggaaa cttaatgaat agattactga ttttcctagt caaagttaat
      841 tcttaccctt ggagtaaaac gaaggtgttt atcctgtgag cctgtgcgtt ttgcatactg
      901 ggttggtttg ctggggctgc ggtgacagca tatgccgcga gctgggcttt aacagagatg
      961 tgtgctctca cagctttgca ggcgggggtc tgagatcagg gtgtcgcggg tggggggtca
     1021 ctgctgaggc cgtgagggga atctgctcag gcctgtccct ggcttctggg ggctgctggt
     1081 ggtattttca gttccttggt gtgtggatac ttcgccccat ctctgccttc acctgtgtcc
     1141 tccctgtgtg ggtgctggtg tccaaaattt ccccttttcg tagtgacacc agctgtgttg
     1201 gattggggcc caccctgctc cagcatggcc taatcttaac taattacatt tgcaaggatc
     1261 ttatgtccac aaaagtcaca gtctgaggtg ctgggggtta ggacttcaat atataaattt
     1321 tgcggttaca caattcaatc catgacagaa tccaaaggtt tactctggtt ataaaaacag
     1381 tacaataaaa tattgtttat agccttccct gtaaggaata ggagagctat tttttattct
     1441 tcccaagatt gtatttgatg taaacatatt ttctgtagaa gccatggccc ttcagttcat
     1501 atagttagaa aatttcctta ttggccaggc acggtggctc acacctgtaa tcccagcact
     1561 ttgggaggcc gaggtgggca gatcacgaag tcaggtgttc gagaccagcc tggccaacat
     1621 ggtgaaatcc cgtctctact aaaaatacaa aaattagctg ggcatggtgg cgcgtgcctg
     1681 taatcccagc tacttggaag gctgaggcag gagaattgct tgaacccggg aggtggaggt
     1741 ttcagtgagc cgagatcaca ccactgcact ccagcctggg caacagagca agactccgtc
     1801 tcaaaaaaag aaaagaaaat gtccttatta cagtctcagg tttctcttgc cctctgtcat
     1861 cctagcagtg tggatggttg gttgggatct tcgtgtcccg tctcagcaca ctcgagctct
     1921 gaagtgaaag tgaggaaggg cagggatggg ggcacttgag cacaccgtgg gccctctgac
     1981 ctcagaccca ggctctgccc caccaagtga ccttgggcag ggtaccttct ctgagctttg
     2041 tttcctcctt ggtaaaggcg gataatagtg tctgccctgc acacagatgt ggacgcagaa
     2101 gcacgtggtg cctgccgggc acaggagtgg tgcacagggc tcgctgctgt cgggagattg
     2161 attgctgttg tggaaacggg agggtactta cagaatgaag cacatttttt acatacagta
     2221 caaatgagtg tgtgcttttt aaatggattt aaaattcaaa tgcaaatctg cagtttaatc
     2281 tcccaagtgc tgatttttct atgtataaag taggagagtg caacagcgta tcggaatgag
     2341 gggctaggga gaacgtgtat gtgacctcga gtacctggca tgtaacagac actcagtatt
     2401 acactcctgc tatttctcca gagcaggtga aacagacggc caggaagcac acgaagagac
     2461 actcagcatc actgcttgtt aaggaaggtg caaatcaaaa ccacagtgag acgccacttc
     2521 acacctacaa gttcggctag atacaaaaag atcgcaacaa gcgtttgcaa ggatgtggag
     2581 aaattggagc cctcacacac tgctggtggc aaagtggtaa cacaggcagg caggtcgtca
     2641 aaaagttaaa catgggccgg gtgcaggtgt ctcaagcctg taatcccagc actttggaag
     2701 gctgagacag gcagattgct tgagcccagg agttcacgac cagcctgggc aacctggtga
     2761 gaccctgtct ctacaaaaaa tacagaacaa ttagctgggc atggtggtgc gtgcctgtgg
     2821 gcccagctac tcggcgggct gaggcaggag gatcacttaa gccccagagg tcaaggctgc
     2881 agtaagccat ggttgtgcca ctgcactcca gcctgggcaa ctgagcaaga ccctgtctca
     2941 aaaaaataaa aaaagataaa catggtgtta ccatttgacc cagcagtttc atacccagga
     3001 gaattgaacg catatgtcca catagaaact cgtacacaga agccaaaatg tggaaaccca
     3061 cgtgtccatc aacagatgaa cggttaaaca aaatgtccat ccatagaacg gaatattatt
     3121 cagtcataaa cagaatgaag tactgtaagt gaaaagccag ttactacata ttgtgtgatt
     3181 ccatttatac ggaatttcta gaataggcac atccatagag acggattagt ggttgcttaa
     3241 gactgggagg gagggggaaa taggaggtga cagctaatgg gcagttttat ttttgatgta
     3301 atgaaaatgt gcttacataa gccgagcagg cataaacaga aaaagtgccc taagattgtg
     3361 ataatggtac aattctgtca attgcataat tggtggatga tgtgtgaatt atgtctctta
     3421 ggataacagc tttactggcg ttaccagaaa aagataaaat aattacattc ca
//
