LOCUS       NM_001031698            3182 bp    mRNA    linear   PRI 22-NOV-2024
DEFINITION  Homo sapiens pre-mRNA processing factor 40 homolog B (PRPF40B),
            transcript variant 1, mRNA.
ACCESSION   NM_001031698
VERSION     NM_001031698.3
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 3182)
  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   2  (bases 1 to 3182)
  AUTHORS   Lorenzini,P.A., Chew,R.S.E., Tan,C.W., Yong,J.Y., Zhang,F.,
            Zheng,J. and Roca,X.
  TITLE     Human PRPF40B regulates hundreds of alternative splicing targets
            and represses a hypoxia expression signature
  JOURNAL   RNA 25 (8), 905-920 (2019)
   PUBMED   31088860
  REMARK    GeneRIF: Study characterizes the transcriptomic regulation of
            PRPF40B in K562 cells upon knockout (KO) and rescue with MDS
            mutations, to reveal a set of targets with weak splice sites and
            A-rich motifs. Importantly, PRPF40B KO up-regulated a hypoxia
            signature which, together with its low expression in AML, suggests
            a role of PRPF40B in myeloid leukemias.
REFERENCE   3  (bases 1 to 3182)
  AUTHORS   Becerra,S., Montes,M., Hernandez-Munain,C. and Sune,C.
  TITLE     Prp40 pre-mRNA processing factor 40 homolog B (PRPF40B) associates
            with SF1 and U2AF65 and modulates alternative pre-mRNA splicing in
            vivo
  JOURNAL   RNA 21 (3), 438-457 (2015)
   PUBMED   25605964
  REMARK    GeneRIF: Placing our data in a functional context, we also show
            that PRPF40B depletion increased Fas/CD95 receptor number and cell
            apoptosis, which suggests the ability of PRPF40B to alter the
            alternative splicing of key apoptotic genes to regulate cell
            survival
REFERENCE   4  (bases 1 to 3182)
  AUTHORS   Buschdorf,J.P. and Stratling,W.H.
  TITLE     A WW domain binding region in methyl-CpG-binding protein MeCP2:
            impact on Rett syndrome
  JOURNAL   J Mol Med (Berl) 82 (2), 135-143 (2004)
   PUBMED   14618241
REFERENCE   5  (bases 1 to 3182)
  AUTHORS   Passani,L.A., Bedford,M.T., Faber,P.W., McGinnis,K.M., Sharp,A.H.,
            Gusella,J.F., Vonsattel,J.P. and MacDonald,M.E.
  TITLE     Huntingtin's WW domain partners in Huntington's disease post-mortem
            brain fulfill genetic criteria for direct involvement in
            Huntington's disease pathogenesis
  JOURNAL   Hum Mol Genet 9 (14), 2175-2182 (2000)
   PUBMED   10958656
REFERENCE   6  (bases 1 to 3182)
  AUTHORS   Faber,P.W., Barnes,G.T., Srinidhi,J., Chen,J., Gusella,J.F. and
            MacDonald,M.E.
  TITLE     Huntingtin interacts with a family of WW domain proteins
  JOURNAL   Hum Mol Genet 7 (9), 1463-1474 (1998)
   PUBMED   9700202
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC020612.40.
            
            On Mar 18, 2020 this sequence version replaced NM_001031698.2.
            
            Summary: This gene encodes a WW-domain containing protein similar
            to yeast splicing factor PRP40. This protein has been shown to
            interact with Huntingtin and methyl CpG binding protein 2 (MeCP2).
            Alternative splicing results in different transcript variants.
            [provided by RefSeq, Aug 2014].
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR14038193.2199603.1,
                                           SRR14038197.1516244.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1968832
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000548825.7/ ENSP00000448073.2
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-33                AC020612.40        97751-97783
            34-114              AC020612.40        104735-104815
            115-258             AC020612.40        105591-105734
            259-324             AC020612.40        106050-106115
            325-352             AC020612.40        106786-106813
            353-378             AC020612.40        107045-107070
            379-489             AC020612.40        107204-107314
            490-610             AC020612.40        107617-107737
            611-635             AC020612.40        107827-107851
            636-842             AC020612.40        108076-108282
            843-966             AC020612.40        108522-108645
            967-1031            AC020612.40        108728-108792
            1032-1196           AC020612.40        109289-109453
            1197-1305           AC020612.40        109555-109663
            1306-1456           AC020612.40        110033-110183
            1457-1590           AC020612.40        110906-111039
            1591-1705           AC020612.40        111660-111774
            1706-1797           AC020612.40        111923-112014
            1798-1914           AC020612.40        116098-116214
            1915-2052           AC020612.40        116425-116562
            2053-2148           AC020612.40        116770-116865
            2149-2235           AC020612.40        117120-117206
            2236-2410           AC020612.40        117413-117587
            2411-2472           AC020612.40        117881-117942
            2473-2616           AC020612.40        118051-118194
            2617-3182           AC020612.40        118290-118855
FEATURES             Location/Qualifiers
     source          1..3182
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="12"
                     /map="12q13.12"
     gene            1..3182
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /note="pre-mRNA processing factor 40 homolog B"
                     /db_xref="GeneID:25766"
                     /db_xref="HGNC:HGNC:25031"
                     /db_xref="MIM:621019"
     exon            1..33
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     CDS             31..2709
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Huntingtin interacting protein C; huntingtin yeast partner
                     C; PRP40 pre-mRNA processing factor 40 homolog B"
                     /codon_start=1
                     /product="pre-mRNA-processing factor 40 homolog B isoform
                     1"
                     /protein_id="NP_001026868.2"
                     /db_xref="CCDS:CCDS31796.2"
                     /db_xref="GeneID:25766"
                     /db_xref="HGNC:HGNC:25031"
                     /db_xref="MIM:621019"
                     /translation="MSVPDSGPRPPAAPAPFPPGPPMMPPPFMPPPGIPPPFPPMGLP
                     PMSQRPPAIPPMPPGILPPMLPPMGAPPPLTQIPGMVPPMMPGMLMPAVPVTAATAPG
                     ADTASSAVAGTGPPRALWSEHVAPDGRIYYYNADDKQSVWEKPSVLKSKAELLLSQCP
                     WKEYKSDTGKPYYYNNQSKESRWTRPKDLDDLEVLVKQEAAGKQQQQLPQTLQPQPPQ
                     PQPDPPPVPPGPTPVPTGLLEPEPGGSEDCDVLEATQPLEQGFLQQLEEGPSSSGQHQ
                     PQQEEEESKPEPERSGLSWSNREKAKQAFKELLRDKAVPSNASWEQAMKMVVTDPRYS
                     ALPKLSEKKQAFNAYKAQREKEEKEEARLRAKEAKQTLQHFLEQHERMTSTTRYRRAE
                     QTFGELEVWAVVPERDRKEVYDDVLFFLAKKEKEQAKQLRRRNIQALKSILDGMSSVN
                     FQTTWSQAQQYLMDNPSFAQDHQLQNMDKEDALICFEEHIRALEREEEEERERARLRE
                     RRQQRKNREAFQTFLDELHETGQLHSMSTWMELYPAVSTDVRFANMLGQPGSTPLDLF
                     KFYVEELKARFHDEKKIIKDILKDRGFCVEVNTAFEDFAHVISFDKRAAALDAGNIKL
                     TFNSLLEKAEAREREREKEEARRMRRREAAFRSMLRQAVPALELGTAWEEVRERFVCD
                     SAFEQITLESERIRLFREFLQVLETECQHLHTKGRKHGRKGKKHHHKRSHSPSGSESE
                     EEELPPPSLRPPKRRRRNPSESGSEPSSSLDSVESGGAALGGRGSPSSHLLGADHGLR
                     KAKKPKKKTKKRRHKSNSPESETDPEEKAGKESDEKEQEQDKDRELQQAELPNRSPGF
                     GIKKEKTGWDTSESELSEGELERRRRTLLQQLDDHQ"
     exon            34..114
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     exon            115..258
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     exon            259..324
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     exon            325..352
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     exon            353..378
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     exon            379..489
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     exon            490..610
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     exon            611..635
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     exon            636..842
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     exon            843..966
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     exon            967..1031
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     exon            1032..1196
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     exon            1197..1305
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     exon            1306..1456
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     exon            1457..1590
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     exon            1591..1705
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     exon            1706..1797
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     exon            1798..1914
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     exon            1915..2052
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     exon            2053..2148
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     exon            2149..2235
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     exon            2236..2410
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     exon            2411..2472
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     exon            2473..2616
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     exon            2617..3182
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /inference="alignment:Splign:2.1.0"
     polyA_site      3182
                     /gene="PRPF40B"
                     /gene_synonym="HYPC"
                     /note="major polyA site"
ORIGIN      
        1 gagccggccc agctgctcgg aggctctggc atgtcggttc ccgattctgg tccccggccc
       61 ccagcagcgc ctgccccctt cccaccgggg ccccccatga tgccaccacc cttcatgccc
      121 cctccaggga tccccccacc ctttcctccg atggggctac cccccatgag tcagagacca
      181 ccagctatcc cccccatgcc acctggcatc ctgcccccaa tgcttccacc aatgggggcg
      241 ccaccaccac tcacacagat accaggaatg gtacctccga tgatgccagg aatgctgatg
      301 ccagcggtgc ctgtcaccgc agcgacggct ccgggtgcgg acaccgccag ctctgctgtg
      361 gctgggacag gccctccgag ggccctatgg agtgagcatg tggccccaga tgggcgcatc
      421 tactactaca atgctgacga caagcagtcc gtgtgggaga agcccagcgt gctcaagtcc
      481 aaggcagagc tgctcctgtc ccaatgtccc tggaaagagt acaagtcgga cacaggcaaa
      541 ccttattact ataacaacca gagtaaagag tcccgctgga cccggcccaa ggatctggat
      601 gacctagagg ttctagtcaa acaagaggct gcagggaaac agcagcagca gctgccacag
      661 acacttcagc cacagccacc tcagccacag cctgaccccc cacctgtgcc tcctggcccc
      721 accccagtgc ccacaggcct cctggaacct gagccaggtg ggagtgaaga ttgtgatgtg
      781 ttggaggcca cccagcccct ggaacagggg ttcctgcagc agctggagga gggccccagc
      841 agttctggac agcatcagcc acagcaggag gaggaggaat caaagccaga accagagagg
      901 tctggcctca gttggagcaa ccgggagaag gcaaagcagg cattcaagga actgctgagg
      961 gacaaggctg tcccctccaa tgcctcatgg gaacaggcca tgaagatggt ggtcaccgac
     1021 ccccgttaca gtgccttgcc taaactgagt gagaaaaagc aggcattcaa tgcctacaag
     1081 gcgcagcggg agaaggagga gaaggaggag gcccggctaa gggccaaaga ggccaagcag
     1141 accctgcagc atttcctgga gcagcatgaa cgcatgacct ccaccacccg ctaccggcgg
     1201 gcagaacaga cctttgggga gctggaggtc tgggctgtgg tccctgagag ggatcgaaaa
     1261 gaggtttatg atgatgtcct cttcttcctg gccaagaagg agaaggaaca ggccaagcag
     1321 ctccggcgcc gcaatatcca ggccctaaag agcatcctgg atgggatgag tagtgtcaac
     1381 ttccaaacca cgtggtccca ggcccagcag tacctcatgg ataaccccag ctttgctcag
     1441 gaccatcagc tgcagaacat ggacaaggaa gatgcactga tctgttttga ggagcacatc
     1501 cgagctttgg agagggaaga ggaggaggaa cgggagcggg cccggcttcg ggagcgacgc
     1561 caacaacgca agaatcggga ggccttccag accttcctgg acgagctgca tgagacaggg
     1621 cagctgcact ctatgtccac ctggatggag ctatatccag cagtcagcac tgatgtccgc
     1681 tttgccaaca tgctgggcca gccgggctcc acccctctgg acttattcaa gttctatgtg
     1741 gaggagttga aggcacgatt ccatgatgaa aagaagatca ttaaggacat ccttaaggac
     1801 cggggcttct gcgtggaggt gaacacggcc tttgaggact tcgcccacgt cataagcttt
     1861 gacaagaggg ctgccgcact ggacgcaggc aacatcaagc tgaccttcaa tagtctgctg
     1921 gagaaagcag aggcacggga gagggagcgg gagaaggagg aggcacgcag gatgcggcgc
     1981 agggaagctg cctttcgaag catgctgagg caggctgtgc ctgctctgga gctaggcact
     2041 gcctgggaag aggtccgtga gcgttttgtg tgtgactcag cctttgagca gatcaccctg
     2101 gagtcggagc ggatccggct cttccgggag ttcctacagg tgctggagac tgaatgccag
     2161 cacctccaca ccaaaggccg aaagcatggc aggaaaggca agaagcacca tcacaagcgt
     2221 tcccactcac cctcaggctc tgagtcagaa gaagaggagc tgcccccacc atctctccgg
     2281 ccccccaagc ggaggaggcg gaacccctca gagtcaggct ctgagccctc ttcctcactt
     2341 gattcagttg aaagtggggg tgctgccctt ggaggacggg gctccccttc ctcccatctt
     2401 cttggagcag atcatggcct tcggaaagcc aagaaaccaa aaaagaaaac taagaagaga
     2461 agacacaagt cgaatagtcc tgagagtgag acagaccctg aggagaaagc tggcaaggag
     2521 agcgatgaga aagaacaaga acaggacaag gacagggagc tccaacaggc agagctccct
     2581 aaccgttccc caggctttgg aatcaagaag gagaagacag gctgggacac gtcagaaagt
     2641 gagctgagtg agggtgagct ggagaggcgg cggcggacac tcctacagca gctggatgat
     2701 caccagtgac ccaatgagct gttctctgcc tcgggtctgt gtgaggccat ggctcctggg
     2761 ccaccctcac cgtctgcctc agacttcttc cttagtctgg tctgtgtcca ctttttctaa
     2821 agtaacccca cccccagcac accattgttg gcacctctca aggttgctct tggtgttcaa
     2881 gggtccccta ctccctggac tagtgcagtc cttgccctca gccccagacc agagatgggt
     2941 ggtatatgcc atgtggggtg ggtgatgcca gtagataaaa gtgtgagaga aggggtctcc
     3001 agggaagagt cacaggctgt tggacgcagc ctgggtggca gagggcaggg tcatcaccct
     3061 ctagcatcag tgcctgctcc tgcctgccct ggccctgagg ctccaccact tcttcctcca
     3121 cccaggacct aatgtacgtg tgttttgttt tttgtttttt aaataacaat atttataaca
     3181 tg
//
