LOCUS       NM_003168               1488 bp    mRNA    linear   PRI 20-SEP-2024
DEFINITION  Homo sapiens SPT4 homolog, DSIF elongation factor subunit
            (SUPT4H1), transcript variant 1, mRNA.
ACCESSION   NM_003168
VERSION     NM_003168.3
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 1488)
  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 1488)
  AUTHORS   Krasnopolsky,S., Novikov,A., Kuzmina,A. and Taube,R.
  TITLE     CRISPRi-mediated depletion of Spt4 and Spt5 reveals a role for DSIF
            in the control of HIV latency
  JOURNAL   Biochim Biophys Acta Gene Regul Mech 1864 (1), 194656 (2021)
   PUBMED   33333262
  REMARK    GeneRIF: CRISPRi-mediated depletion of Spt4 and Spt5 reveals a role
            for DSIF in the control of HIV latency.
REFERENCE   3  (bases 1 to 1488)
  AUTHORS   Fragoza,R., Das,J., Wierbowski,S.D., Liang,J., Tran,T.N., Liang,S.,
            Beltran,J.F., Rivera-Erick,C.A., Ye,K., Wang,T.Y., Yao,L., Mort,M.,
            Stenson,P.D., Cooper,D.N., Wei,X., Keinan,A., Schimenti,J.C.,
            Clark,A.G. and Yu,H.
  TITLE     Extensive disruption of protein interactions by genetic variants
            across the allele frequency spectrum in human populations
  JOURNAL   Nat Commun 10 (1), 4141 (2019)
   PUBMED   31515488
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 1488)
  AUTHORS   Naguib,A., Sandmann,T., Yi,F., Watts,R.J., Lewcock,J.W. and
            Dowdle,W.E.
  TITLE     SUPT4H1 Depletion Leads to a Global Reduction in RNA
  JOURNAL   Cell Rep 26 (1), 45-53 (2019)
   PUBMED   30605685
  REMARK    GeneRIF: Authors depleted SUPT4H1 by RNA interference to inhibit
            the function of the SUPT4H1/SUPT5H transcription elongation
            complex. Depletion of SUPT4H1 leads to a global reduction in all
            cellular RNA.
REFERENCE   5  (bases 1 to 1488)
  AUTHORS   Kramer,N.J., Carlomagno,Y., Zhang,Y.J., Almeida,S., Cook,C.N.,
            Gendron,T.F., Prudencio,M., Van Blitterswijk,M., Belzil,V.,
            Couthouis,J., Paul,J.W. 3rd, Goodman,L.D., Daughrity,L., Chew,J.,
            Garrett,A., Pregent,L., Jansen-West,K., Tabassian,L.J.,
            Rademakers,R., Boylan,K., Graff-Radford,N.R., Josephs,K.A.,
            Parisi,J.E., Knopman,D.S., Petersen,R.C., Boeve,B.F., Deng,N.,
            Feng,Y., Cheng,T.H., Dickson,D.W., Cohen,S.N., Bonini,N.M.,
            Link,C.D., Gao,F.B., Petrucelli,L. and Gitler,A.D.
  TITLE     Spt4 selectively regulates the expression of C9orf72 sense and
            antisense mutant transcripts
  JOURNAL   Science 353 (6300), 708-712 (2016)
   PUBMED   27516603
  REMARK    GeneRIF: Knockdown of SUPT4H1, the human Spt4 ortholog, similarly
            decreased production of sense and antisense RNA foci, as well as
            dipeptide repeat proteins, in patient cells.
REFERENCE   6  (bases 1 to 1488)
  AUTHORS   Wada,T., Takagi,T., Yamaguchi,Y., Watanabe,D. and Handa,H.
  TITLE     Evidence that P-TEFb alleviates the negative effect of DSIF on RNA
            polymerase II-dependent transcription in vitro
  JOURNAL   EMBO J 17 (24), 7395-7403 (1998)
   PUBMED   9857195
REFERENCE   7  (bases 1 to 1488)
  AUTHORS   Wada,T., Takagi,T., Yamaguchi,Y., Ferdous,A., Imai,T., Hirose,S.,
            Sugimoto,S., Yano,K., Hartzog,G.A., Winston,F., Buratowski,S. and
            Handa,H.
  TITLE     DSIF, a novel transcription elongation factor that regulates RNA
            polymerase II processivity, is composed of human Spt4 and Spt5
            homologs
  JOURNAL   Genes Dev 12 (3), 343-356 (1998)
   PUBMED   9450929
REFERENCE   8  (bases 1 to 1488)
  AUTHORS   Chiang,P.W., Wang,S.Q., Smithivas,P., Song,W.J., Crombez,E.,
            Akhtar,A., Im,R., Greenfield,J., Ramamoorthy,S., Van Keuren,M.,
            Blackburn,C.C., Tsai,C.H. and Kurnit,D.M.
  TITLE     Isolation and characterization of the human and mouse homologues
            (SUPT4H and Supt4h) of the yeast SPT4 gene
  JOURNAL   Genomics 34 (3), 368-375 (1996)
   PUBMED   8786137
REFERENCE   9  (bases 1 to 1488)
  AUTHORS   Hartzog,G.A., Basrai,M.A., Ricupero-Hovasse,S.L., Hieter,P. and
            Winston,F.
  TITLE     Identification and analysis of a functional human homolog of the
            SPT4 gene of Saccharomyces cerevisiae
  JOURNAL   Mol Cell Biol 16 (6), 2848-2856 (1996)
   PUBMED   8649394
REFERENCE   10 (bases 1 to 1488)
  AUTHORS   Adams,M.D., Kerlavage,A.R., Fleischmann,R.D., Fuldner,R.A.,
            Bult,C.J., Lee,N.H., Kirkness,E.F., Weinstock,K.G., Gocayne,J.D.,
            White,O. et al.
  TITLE     Initial assessment of human gene diversity and expression patterns
            based upon 83 million nucleotides of cDNA sequence
  JOURNAL   Nature 377 (6547 Suppl), 3-174 (1995)
   PUBMED   7566098
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from U43923.1 and BG026473.1.
            
            On Nov 22, 2018 this sequence version replaced NM_003168.2.
            
            Summary: This gene encodes the small subunit of DRB
            (5,6-dichloro-1-beta-d-ribofuranosylbenzimidazole)
            sensitivity-inducing factor (DSIF) complex, which regulates mRNA
            processing and transcription elongation by RNA polymerase II. The
            encoded protein is localized to the nucleus and interacts with the
            large subunit (SUPT5H) to form the DSIF complex. Related
            pseudogenes have been identified on chromosomes 2 and 12.
            Alternatively spliced transcript variants have been found for this
            gene. [provided by RefSeq, Nov 2012].
            
            Transcript Variant: This variant (1) represents the shorter
            transcript and encodes the functional protein.
            
            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 :: U43923.1, SRR5189652.103830.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968540, SAMEA2149004
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000225504.8/ ENSP00000225504.3
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-912               U43923.1           2-913
            913-1400            BG026473.1         115-602
            1401-1488           U43923.1           1402-1489
FEATURES             Location/Qualifiers
     source          1..1488
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="17"
                     /map="17q22"
     gene            1..1488
                     /gene="SUPT4H1"
                     /gene_synonym="SPT4; SPT4H; Supt4a; SUPT4H"
                     /note="SPT4 homolog, DSIF elongation factor subunit"
                     /db_xref="GeneID:6827"
                     /db_xref="HGNC:HGNC:11467"
                     /db_xref="MIM:603555"
     exon            1..135
                     /gene="SUPT4H1"
                     /gene_synonym="SPT4; SPT4H; Supt4a; SUPT4H"
                     /inference="alignment:Splign:2.1.0"
     CDS             67..420
                     /gene="SUPT4H1"
                     /gene_synonym="SPT4; SPT4H; Supt4a; SUPT4H"
                     /note="small hSpt4 subunit; DSIF p14; DRB
                     sensitivity-inducing factor 14 kDa subunit; suppressor of
                     Ty 4 homolog 1"
                     /codon_start=1
                     /product="transcription elongation factor SPT4"
                     /protein_id="NP_003159.1"
                     /db_xref="CCDS:CCDS11606.1"
                     /db_xref="GeneID:6827"
                     /db_xref="HGNC:HGNC:11467"
                     /db_xref="MIM:603555"
                     /translation="MALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKG
                     NREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRLPQGIVRELK
                     SRGVAYKSRDTAIKT"
     exon            136..242
                     /gene="SUPT4H1"
                     /gene_synonym="SPT4; SPT4H; Supt4a; SUPT4H"
                     /inference="alignment:Splign:2.1.0"
     exon            243..298
                     /gene="SUPT4H1"
                     /gene_synonym="SPT4; SPT4H; Supt4a; SUPT4H"
                     /inference="alignment:Splign:2.1.0"
     exon            299..352
                     /gene="SUPT4H1"
                     /gene_synonym="SPT4; SPT4H; Supt4a; SUPT4H"
                     /inference="alignment:Splign:2.1.0"
     exon            353..1488
                     /gene="SUPT4H1"
                     /gene_synonym="SPT4; SPT4H; Supt4a; SUPT4H"
                     /inference="alignment:Splign:2.1.0"
     regulatory      718..723
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SUPT4H1"
                     /gene_synonym="SPT4; SPT4H; Supt4a; SUPT4H"
                     /note="hexamer: AATAAA"
     polyA_site      755
                     /gene="SUPT4H1"
                     /gene_synonym="SPT4; SPT4H; Supt4a; SUPT4H"
                     /note="major polyA site"
     regulatory      1463..1468
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SUPT4H1"
                     /gene_synonym="SPT4; SPT4H; Supt4a; SUPT4H"
                     /note="hexamer: TATAAA"
     polyA_site      1488
                     /gene="SUPT4H1"
                     /gene_synonym="SPT4; SPT4H; Supt4a; SUPT4H"
ORIGIN      
        1 atttacttcc tgcgggtgca caggctgtgg tcgtctatct ccctgttgtt cttcccatcg
       61 gcgaagatgg ccctggagac ggtgccgaag gacctgcggc atctgcgggc ctgtttgctg
      121 tgttcgctgg tcaagactat agaccagttt gaatatgatg gttgtgacaa ttgtgatgca
      181 tatctacaaa tgaagggtaa ccgagagatg gtatatgact gcactagctc ttcctttgat
      241 ggaatcattg cgatgatgag tccagaggac agctgggtct ccaagtggca gcgagtcagt
      301 aactttaagc caggtgtata tgcggtgtca gtcactggtc gcctgcccca aggaatcgtg
      361 cgggagctga aaagtcgagg agtggcctac aaatccagag acacagctat aaagacctag
      421 caagatgcaa ggctgccagc atctttgctc tccacctcct gcctctgctt atttcttgtt
      481 ctggaactaa atgaacagaa cttcaaatac ttcctaccct ccaattcaga ctcagctgac
      541 tgttgagaga gcagcacatc attttatcat tttatcttct ttggactaca ggtggggtgg
      601 gagggatttg ggttggtgga ttaacagatg gaattgagga gagagtagga tgctgatttt
      661 cctacccgtg gcccaggtct gtgccttccc catgccaagg actctaggtc aaatgtcaat
      721 aaatatgaac ctcgagaaag ttctgaaggc catgacacct gccttgcctc cctcttccat
      781 tctcttaggc acagtaatag cttatttgcc ctataagaac cttcccagag cagcagaggc
      841 ccttctactc cctcttgact gtctcagcct ctgggattgc agcctttgta gtgtgcttcc
      901 ttgcttccta tcggagggtg ctgatccaga ggctcagtaa ccccatcaac ttggtggccc
      961 tggtgtctca cacttgtatc cttctgccct cgagacctgg cacagcagta tcccttgaag
     1021 aaatcctgag gctttgtaga gtgctccttg accatgttta ataattcttc cctcccctgc
     1081 ttgtctattt tcttctcttc acggctcttc ctatacctta ggccagtctc aagcactcac
     1141 tggagaccct tgggccttgg gcgaccattg agtcctagtc tcccttgttt gtgcccctgt
     1201 aggaggtagg tccttttctc ctccggccta gtaggggacc ttgggtaaca tcccattttt
     1261 cggccaaggt gagttgtttt aggataaaaa aatttaccac aaattctcat ttaaatttcc
     1321 acagaaatcc tgttcgtatc cccattttga tttccctaag ttccttgttc tccctctaaa
     1381 aagagaatga ttgcaccctg cctgtttacc tcaggattgt tgtgattgta gaaacgaagc
     1441 tatgtgaaaa ttatataagt attataaagg tgaaatactt ttgctctc
//
