LOCUS       NM_021393               2650 bp    mRNA    linear   ROD 01-AUG-2024
DEFINITION  Mus musculus negative elongation factor complex member B (Nelfb),
            transcript variant 1, mRNA.
ACCESSION   NM_021393
VERSION     NM_021393.3
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 2650)
  AUTHORS   Kaye,E.G., Basavaraju,K., Nelson,G.M., Zomer,H.D., Roy,D.,
            Joseph,I.I., Rajabi-Toustani,R., Qiao,H., Adelman,K. and Reddi,P.P.
  TITLE     RNA polymerase II pausing is essential during spermatogenesis for
            appropriate gene expression and completion of meiosis
  JOURNAL   Nat Commun 15 (1), 848 (2024)
   PUBMED   38287033
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2650)
  AUTHORS   Pan,H., Cheng,X., Rodriguez,P.F.G., Zhang,X., Chung,I., Jin,V.X.,
            Li,W., Hu,Y. and Li,R.
  TITLE     An essential signaling function of cytoplasmic NELFB is independent
            of RNA polymerase II pausing
  JOURNAL   J Biol Chem 299 (11), 105259 (2023)
   PUBMED   37717699
  REMARK    GeneRIF: An essential signaling function of cytoplasmic NELFB is
            independent of RNA polymerase II pausing.
REFERENCE   3  (bases 1 to 2650)
  AUTHORS   Abe,K., Schauer,T. and Torres-Padilla,M.E.
  TITLE     Distinct patterns of RNA polymerase II and transcriptional
            elongation characterize mammalian genome activation
  JOURNAL   Cell Rep 41 (13), 111865 (2022)
   PUBMED   36577375
REFERENCE   4  (bases 1 to 2650)
  AUTHORS   Abuhashem,A., Chivu,A.G., Zhao,Y., Rice,E.J., Siepel,A., Danko,C.G.
            and Hadjantonakis,A.K.
  TITLE     RNA Pol II pausing facilitates phased pluripotency transitions by
            buffering transcription
  JOURNAL   Genes Dev 36 (13-14), 770-789 (2022)
   PUBMED   35981753
  REMARK    Publication Status: Available-Online prior to print
REFERENCE   5  (bases 1 to 2650)
  AUTHORS   Pan,H., Zhao,X., Zhang,X., Abouelsoud,M., Sun,J., April,C.,
            Amleh,A., Fan,J.B., Hu,Y. and Li,R.
  TITLE     Translational Initiation at a Non-AUG Start Codon for Human and
            Mouse Negative Elongation Factor-B
  JOURNAL   PLoS One 10 (5), e0127422 (2015)
   PUBMED   26010750
  REMARK    GeneRIF: both human and mouse NELF-B proteins are translated from a
            non-AUG codon upstream of the annotated AUG.
            GeneRIF: Human and mouse Nelfb encode proteins translated from a
            non-AUG (CUG) start codon. The majority of mouse tissues examined
            express the isoform translated from the CUG start codon, but a
            small number of tissues also express a shorter isoform of the same
            apparent size as the AUG-initiated isoform.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 2650)
  AUTHORS   Pan,H., Qin,K., Guo,Z., Ma,Y., April,C., Gao,X., Andrews,T.G.,
            Bokov,A., Zhang,J., Chen,Y., Weintraub,S.T., Fan,J.B., Wang,D.,
            Hu,Y., Aune,G.J., Lindsey,M.L. and Li,R.
  TITLE     Negative elongation factor controls energy homeostasis in
            cardiomyocytes
  JOURNAL   Cell Rep 7 (1), 79-85 (2014)
   PUBMED   24656816
REFERENCE   7  (bases 1 to 2650)
  AUTHORS   Ichim,G., Genevois,A.L., Menard,M., Yu,L.Y., Coelho-Aguiar,J.M.,
            Llambi,F., Jarrosson-Wuilleme,L., Lefebvre,J., Tulasne,D.,
            Dupin,E., Le Douarin,N., Arumae,U., Tauszig-Delamasure,S. and
            Mehlen,P.
  TITLE     The dependence receptor TrkC triggers mitochondria-dependent
            apoptosis upon Cobra-1 recruitment
  JOURNAL   Mol Cell 51 (5), 632-646 (2013)
   PUBMED   24034695
  REMARK    GeneRIF: Cobra1 Is Required for TrkC-Induced Apoptosis.
REFERENCE   8  (bases 1 to 2650)
  AUTHORS   Gupte,R., Muse,G.W., Chinenov,Y., Adelman,K. and Rogatsky,I.
  TITLE     Glucocorticoid receptor represses proinflammatory genes at distinct
            steps of the transcription cycle
  JOURNAL   Proc Natl Acad Sci U S A 110 (36), 14616-14621 (2013)
   PUBMED   23950223
REFERENCE   9  (bases 1 to 2650)
  AUTHORS   Sun,J., Pan,H., Lei,C., Yuan,B., Nair,S.J., April,C.,
            Parameswaran,B., Klotzle,B., Fan,J.B., Ruan,J. and Li,R.
  TITLE     Genetic and genomic analyses of RNA polymerase II-pausing factor in
            regulation of mammalian transcription and cell growth
  JOURNAL   J Biol Chem 286 (42), 36248-36257 (2011)
   PUBMED   21865163
  REMARK    GeneRIF: genetic and genomic studies provide new physiological and
            molecular insight into Nelf-mediated pol II pausing.
REFERENCE   10 (bases 1 to 2650)
  AUTHORS   Amleh,A., Nair,S.J., Sun,J., Sutherland,A., Hasty,P. and Li,R.
  TITLE     Mouse cofactor of BRCA1 (Cobra1) is required for early
            embryogenesis
  JOURNAL   PLoS One 4 (4), e5034 (2009)
   PUBMED   19340312
  REMARK    GeneRIF: findings also indicate that Cobra1 helps maintain the
            undifferentiated state of mESCs by preventing unscheduled
            expression of developmental genes
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AL732309.9, CJ100279.1,
            AK173124.1 and AI843129.1.
            
            On Jul 3, 2015 this sequence version replaced NM_021393.2.
            
            Summary: This gene encodes subunit B of a metazoan-specific,
            four-subunit protein complex that regulates promoter-proximal
            pausing of RNA polymerase II. RNA polymerase II pausing is thought
            to be important for coordination of gene transcription during
            embryonic development and stress responses. Consistently,
            disruption of this gene in mouse causes inner cell mass deficiency
            and embryonic lethality. In addition, this gene is required for
            maintenance of mouse embryonic stem cells by preventing expression
            of developmental genes. In adult mice, conditional deletion of this
            gene results in cardiomyopathy and impaired response to cardiac
            stress. Multiple protein isoforms are encoded through the use of a
            non-AUG (CUG) initiation codon and an alternative downstream AUG
            initiation codon. In addition, alternative splicing results in
            multiple transcript variants. [provided by RefSeq, Jul 2015].
            
            Transcript Variant: This variant (1) represents the longer isoform
            (1), which is translated using a non-AUG (CUG) start codon.
            
            CCDS Note: The coding region has been updated to extend the protein
            N-terminus and to use a non-AUG (CUG) start codon, supported by
            data in PMID:26010750.
            
            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 :: BC004762.1, AK087524.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMN00849374,
                                           SAMN00849375 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            non-AUG initiation codon :: PMID: 26010750
            RefSeq Select criteria   :: based on conservation, expression,
                                        longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-57                AL732309.9         104065-104121       c
            58-465              CJ100279.1         2-409
            466-2630            AK173124.1         1-2165
            2631-2650           AI843129.1         4-23                c
FEATURES             Location/Qualifiers
     source          1..2650
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="2"
                     /map="2 17.06 cM"
     gene            1..2650
                     /gene="Nelfb"
                     /gene_synonym="A730008L03Rik; Cobra1; Nelf-b"
                     /note="negative elongation factor complex member B"
                     /db_xref="GeneID:58202"
                     /db_xref="MGI:MGI:1931035"
     exon            1..388
                     /gene="Nelfb"
                     /gene_synonym="A730008L03Rik; Cobra1; Nelf-b"
                     /inference="alignment:Splign:2.1.0"
     CDS             143..2029
                     /gene="Nelfb"
                     /gene_synonym="A730008L03Rik; Cobra1; Nelf-b"
                     /note="isoform 1 is encoded by transcript variant 1;
                     non-AUG (CUG) translation initiation codon; ortholog of
                     human cofactor of BRCA1 (COBRA1); negative elongation
                     factor complex member B, Cobra1"
                     /codon_start=1
                     /product="negative elongation factor B isoform 1"
                     /protein_id="NP_067368.3"
                     /db_xref="CCDS:CCDS15751.2"
                     /db_xref="GeneID:58202"
                     /db_xref="MGI:MGI:1931035"
                     /translation="MEAAGERGLGGPRGTVERASGAPSGSATAPAERGGDGVHSRASA
                     GASAMFAGLQDLGVANGEDLKETLTNCTEPLKAIEQFQTENGVLLPSLQSALPFLDLH
                     GTPRLEFHQSVFDELRDKLLERVSAIASEGKAEERYKKLEDLLEKSFSLVKMPSLQPV
                     VMCVMKHLPKVPEKKLKLVMADKELYRACAVEVKRQIWQDNQALFGDEVSPLLKQYIL
                     EKESALFSTELSVLHNFFSPSPKTRRQGEVVQKLTQMVGKNVKLYDMVLQFLRTLFLR
                     TRNVHYCTLRAELLMSLHDLDVSDICTVDPCHKFTWCLDACIRERFVDSKRARELQGF
                     LDGVKKGQEQVLGDLSMILCDPFAINTLSLSTIRHLQELVSQETLPRDSPDLLLLLRL
                     LALGQGAWDLIDSQVFKEPKMEAELITKFLPMLMSLVVDDFTFNVDQKLPAEEKASVT
                     YPNTLPESFTKFLQEQRMACEVGLYYVLHITKQRNKNALLRLLPGLVETFGDLAFSDI
                     FLHLLTGSLVLLADEFALEDFCSSLFDGFFLTASPRKENVHRHVLRLLLHLHARVAPS
                     KLEALQKALEPTGQSGEAVKELYSQLGEKLEQLDHRKPSPTQAAETPALDLPLPSVPA
                     PATL"
     exon            389..552
                     /gene="Nelfb"
                     /gene_synonym="A730008L03Rik; Cobra1; Nelf-b"
                     /inference="alignment:Splign:2.1.0"
     exon            553..652
                     /gene="Nelfb"
                     /gene_synonym="A730008L03Rik; Cobra1; Nelf-b"
                     /inference="alignment:Splign:2.1.0"
     exon            653..883
                     /gene="Nelfb"
                     /gene_synonym="A730008L03Rik; Cobra1; Nelf-b"
                     /inference="alignment:Splign:2.1.0"
     exon            884..1069
                     /gene="Nelfb"
                     /gene_synonym="A730008L03Rik; Cobra1; Nelf-b"
                     /inference="alignment:Splign:2.1.0"
     exon            1070..1182
                     /gene="Nelfb"
                     /gene_synonym="A730008L03Rik; Cobra1; Nelf-b"
                     /inference="alignment:Splign:2.1.0"
     exon            1183..1285
                     /gene="Nelfb"
                     /gene_synonym="A730008L03Rik; Cobra1; Nelf-b"
                     /inference="alignment:Splign:2.1.0"
     exon            1286..1381
                     /gene="Nelfb"
                     /gene_synonym="A730008L03Rik; Cobra1; Nelf-b"
                     /inference="alignment:Splign:2.1.0"
     exon            1382..1524
                     /gene="Nelfb"
                     /gene_synonym="A730008L03Rik; Cobra1; Nelf-b"
                     /inference="alignment:Splign:2.1.0"
     exon            1525..1631
                     /gene="Nelfb"
                     /gene_synonym="A730008L03Rik; Cobra1; Nelf-b"
                     /inference="alignment:Splign:2.1.0"
     exon            1632..1773
                     /gene="Nelfb"
                     /gene_synonym="A730008L03Rik; Cobra1; Nelf-b"
                     /inference="alignment:Splign:2.1.0"
     exon            1774..1882
                     /gene="Nelfb"
                     /gene_synonym="A730008L03Rik; Cobra1; Nelf-b"
                     /inference="alignment:Splign:2.1.0"
     exon            1883..2637
                     /gene="Nelfb"
                     /gene_synonym="A730008L03Rik; Cobra1; Nelf-b"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2613..2618
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Nelfb"
                     /gene_synonym="A730008L03Rik; Cobra1; Nelf-b"
                     /note="hexamer: AATAAA"
     polyA_site      2633
                     /gene="Nelfb"
                     /gene_synonym="A730008L03Rik; Cobra1; Nelf-b"
                     /note="major polyA site"
ORIGIN      
        1 tgggtagcaa gtcgctgctc ggaacctgcg ggcggcggag gcgttttccc ggggcctatt
       61 ggctgctgga cctaggcagt caagggcgga agtgggaggt gtgggtccgt gcgagctgct
      121 ctgctgacgc gatctggcca cactggaggc ggcgggcgaa cggggcttgg ggggtcctcg
      181 tggcaccgtg gagagggctt ctggggctcc gtcagggtcc gctacggctc cagcggagcg
      241 cggtggggat ggggtacaca gccgagcgtc cgccggagcc tccgccatgt tcgcggggct
      301 ccaggacctg ggcgtggcca atggcgagga cctgaaagag accctgacca actgcaccga
      361 gcctctcaag gccattgaac aatttcagac agagaatggc gtgttgctgc cttccctgca
      421 gtcggccctg cccttcttgg atctacacgg gacaccgcgg ctggagttcc atcagtcagt
      481 gtttgatgaa ctacgtgaca aacttctgga acgagtgtca gcaattgcct ctgagggaaa
      541 ggcagaggag aggtacaaga agctggaaga ccttctggaa aagagctttt ctttggtcaa
      601 gatgccatcc ctacaaccag tggtgatgtg tgttatgaaa cacttgccca aggttcctga
      661 gaagaagctg aagctggtga tggctgacaa ggagttgtac cgggcatgtg ctgtggaagt
      721 gaagaggcag atttggcaag acaaccaggc tctctttggt gatgaagtct caccactgct
      781 gaagcagtat atcctagaga aagagagtgc gctcttcagc acagagctct ctgtgctgca
      841 caacttcttc agcccttccc ccaagacccg gcgccaagga gaggtggtgc agaagctgac
      901 gcagatggta gggaagaatg tgaagctgta cgacatggtg ctgcagttcc tgcgcacact
      961 gttcctgcgg accaggaatg tgcactactg cacgttacga gctgagctgc tcatgtcttt
     1021 gcatgacttg gacgtcagtg acatctgcac tgtggatccc tgccataagt tcacctggtg
     1081 cctggatgcc tgcatccggg aacggtttgt ggacagcaaa agagcccggg agcttcaggg
     1141 atttcttgat ggtgtgaaga agggccagga acaagttttg ggggatttgt ctatgatcct
     1201 gtgcgacccc tttgccatca acacactgtc cctgagcacc atcaggcact tgcaggagct
     1261 ggttagccag gagacactgc ccagggatag tcccgacctc ctcctactac ttaggctgct
     1321 ggcactgggc caaggtgcat gggacttaat agatagccag gtcttcaagg agcctaagat
     1381 ggaggcagag ctcatcacca agttcctgcc gatgctcatg tccctcgtgg tggatgactt
     1441 cactttcaac gtagatcaga agcttccagc tgaggagaaa gcctcagtca cataccccaa
     1501 cacacttcct gagagtttca ccaagtttct gcaggagcag cgcatggctt gtgaggtggg
     1561 actatactac gtcctacaca tcaccaagca gagaaacaag aatgctctcc tgcgcctgct
     1621 gcctggactt gtggaaacgt ttggtgacct ggccttcagt gacatctttc tccacctgct
     1681 cactgggagc ctggtactgc ttgctgatga atttgccctg gaggatttct gcagcagcct
     1741 ctttgatggc ttcttcctca ctgcctctcc caggaaggag aatgtgcacc gtcatgtgct
     1801 gaggcttctc ctccacttgc atgcaagagt ggccccttcc aagctggagg cattgcagaa
     1861 ggctctggag cccacaggcc agagcgggga ggccgtgaag gagctctact cccagcttgg
     1921 tgagaagttg gagcagttag accatcgaaa gcccagtcct acccaagctg cagagacacc
     1981 agcactggat ctgcctcttc ccagcgtgcc tgctccagcc acactgtgag gctgtggaga
     2041 actgaaactg tttgacagtg gtgccctatg gaagggcacc tagttggcta ggggtgtagg
     2101 ctgagctgag aggggtgttc tttggcaagg ttctccctcc tctagtttct cccaggagct
     2161 ggtcccaaaa ggtcctccct cagtggtcta cttgcatatc atagggggcc cttgatgtca
     2221 tggtgggact tggcccctgc ttgaccctgg cagaggtgga tggtgattgg gatataggaa
     2281 aagcagtggg cagaggcctg actgacctga tattcaatct gcacaaagtc caaggtatgc
     2341 taggttcacc aaagtagatt tgctggacct gatccccaag cacaggagtg gtaccctcca
     2401 cagaagctgg gggagagtct gcagcaggcc tgagcctgct gatgtcagtg ctgactgagt
     2461 ccatgctaac tgagatctgt aggcagagct ctgccctgta gctccctgcc tcagtttatc
     2521 tttgcaatac aaagcaaatc cttccccagc tatgtgtttt agcctttgag taggggagtt
     2581 tcggtgtaca cattgaattt tccacttatg taaataaaac ggattttgat aaatccaaaa
     2641 aaaaaaaaaa
//
