LOCUS       NM_001398656            1314 bp    mRNA    linear   ROD 31-MAR-2024
DEFINITION  Rattus norvegicus cyclin-dependent kinase 7 (Cdk7), transcript
            variant 1, mRNA.
ACCESSION   NM_001398656 XM_039103488
VERSION     NM_001398656.1
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Rattus.
REFERENCE   1  (bases 1 to 1314)
  AUTHORS   Jeronimo,C., Bataille,A.R. and Robert,F.
  TITLE     The writers, readers, and functions of the RNA polymerase II
            C-terminal domain code
  JOURNAL   Chem Rev 113 (11), 8491-8522 (2013)
   PUBMED   23837720
  REMARK    Review article
REFERENCE   2  (bases 1 to 1314)
  AUTHORS   Wang,Y., Liu,F., Mao,F., Hang,Q., Huang,X., He,S., Wang,Y.,
            Cheng,C., Wang,H., Xu,G., Zhang,T. and Shen,A.
  TITLE     Interaction with cyclin H/cyclin-dependent kinase 7 (CCNH/CDK7)
            stabilizes C-terminal binding protein 2 (CtBP2) and promotes cancer
            cell migration
  JOURNAL   J Biol Chem 288 (13), 9028-9034 (2013)
   PUBMED   23393140
REFERENCE   3  (bases 1 to 1314)
  AUTHORS   Egloff,S., Dienstbier,M. and Murphy,S.
  TITLE     Updating the RNA polymerase CTD code: adding gene-specific layers
  JOURNAL   Trends Genet 28 (7), 333-341 (2012)
   PUBMED   22622228
  REMARK    Review article
REFERENCE   4  (bases 1 to 1314)
  AUTHORS   Fujii,W., Nishimura,T., Kano,K., Sugiura,K. and Naito,K.
  TITLE     CDK7 and CCNH are components of CDK-activating kinase and are
            required for meiotic progression of pig oocytes
  JOURNAL   Biol Reprod 85 (6), 1124-1132 (2011)
   PUBMED   21778139
REFERENCE   5  (bases 1 to 1314)
  AUTHORS   Egly,J.M. and Coin,F.
  TITLE     A history of TFIIH: two decades of molecular biology on a pivotal
            transcription/repair factor
  JOURNAL   DNA Repair (Amst) 10 (7), 714-721 (2011)
   PUBMED   21592869
  REMARK    Review article
REFERENCE   6  (bases 1 to 1314)
  AUTHORS   Kershnar,E., Wu,S.Y. and Chiang,C.M.
  TITLE     Immunoaffinity purification and functional characterization of
            human transcription factor IIH and RNA polymerase II from clonal
            cell lines that conditionally express epitope-tagged subunits of
            the multiprotein complexes
  JOURNAL   J Biol Chem 273 (51), 34444-34453 (1998)
   PUBMED   9852112
REFERENCE   7  (bases 1 to 1314)
  AUTHORS   Reardon,J.T., Ge,H., Gibbs,E., Sancar,A., Hurwitz,J. and Pan,Z.Q.
  TITLE     Isolation and characterization of two human transcription factor
            IIH (TFIIH)-related complexes: ERCC2/CAK and TFIIH
  JOURNAL   Proc Natl Acad Sci U S A 93 (13), 6482-6487 (1996)
   PUBMED   8692841
  REMARK    Erratum:[Proc Natl Acad Sci U S A 1996 Sep 17;93(19):10538]
REFERENCE   8  (bases 1 to 1314)
  AUTHORS   Weiler,M.C., Smith,J.L. and Masters,J.N.
  TITLE     CR16, a novel proline-rich protein expressed in rat brain neurons,
            binds to SH3 domains and is a MAP kinase substrate
  JOURNAL   J Mol Neurosci 7 (3), 203-215 (1996)
   PUBMED   8906616
REFERENCE   9  (bases 1 to 1314)
  AUTHORS   Ossipow,V., Tassan,J.P., Nigg,E.A. and Schibler,U.
  TITLE     A mammalian RNA polymerase II holoenzyme containing all components
            required for promoter-specific transcription initiation
  JOURNAL   Cell 83 (1), 137-146 (1995)
   PUBMED   7553866
REFERENCE   10 (bases 1 to 1314)
  AUTHORS   Serizawa,H., Makela,T.P., Conaway,J.W., Conaway,R.C., Weinberg,R.A.
            and Young,R.A.
  TITLE     Association of Cdk-activating kinase subunits with transcription
            factor TFIIH
  JOURNAL   Nature 374 (6519), 280-282 (1995)
   PUBMED   7885450
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000002.1.
            
            On Dec 21, 2021 this sequence version replaced XM_039103488.1.
            
            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 :: SRR26643298.9380.1,
                                           SRR26360176.2117034.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA5760383,
                                           SAMEA5760389 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-172               JAXUCZ010000002.1  33599314-33599485   c
            173-232             JAXUCZ010000002.1  33598993-33599052   c
            233-266             JAXUCZ010000002.1  33593218-33593251   c
            267-334             JAXUCZ010000002.1  33591851-33591918   c
            335-403             JAXUCZ010000002.1  33589803-33589871   c
            404-514             JAXUCZ010000002.1  33586594-33586704   c
            515-633             JAXUCZ010000002.1  33585525-33585643   c
            634-733             JAXUCZ010000002.1  33582765-33582864   c
            734-820             JAXUCZ010000002.1  33581125-33581211   c
            821-970             JAXUCZ010000002.1  33577478-33577627   c
            971-1118            JAXUCZ010000002.1  33575715-33575862   c
            1119-1314           JAXUCZ010000002.1  33574623-33574818   c
FEATURES             Location/Qualifiers
     source          1..1314
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="2"
                     /map="2q12"
     gene            1..1314
                     /gene="Cdk7"
                     /gene_synonym="CAK; P39 Mo15"
                     /note="cyclin-dependent kinase 7"
                     /db_xref="GeneID:171150"
                     /db_xref="RGD:621124"
     exon            1..172
                     /gene="Cdk7"
                     /gene_synonym="CAK; P39 Mo15"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    23..25
                     /gene="Cdk7"
                     /gene_synonym="CAK; P39 Mo15"
                     /note="upstream in-frame stop codon"
     CDS             107..1147
                     /gene="Cdk7"
                     /gene_synonym="CAK; P39 Mo15"
                     /EC_number="2.7.11.23"
                     /EC_number="2.7.11.22"
                     /note="isoform 1 is encoded by transcript variant 1; cell
                     division protein kinase 7; 39 protein kinase;
                     CDK-activating kinase 1; TFIIH basal transcription factor
                     complex kinase subunit; cyclin-dependent kinase 7 (MO15
                     homolog, Xenopus laevis, cdk-activating kinase);
                     cyclin-dependent kinase 7 (homolog of Xenopus MO15
                     cdk-activating kinase)"
                     /codon_start=1
                     /product="cyclin-dependent kinase 7 isoform 1"
                     /protein_id="NP_001385585.1"
                     /db_xref="GeneID:171150"
                     /db_xref="RGD:621124"
                     /translation="

MAVDVKSRAKRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRSEAKDGINRTALREIKLLQELSHPNIIGLLDAFGHKSNISLVFDFMETDLEVIIKDNSLVLTPSHIKAYMLMTLQGLEYLHQHWILHRDLKPNNLLLDENGVLKLADFGLAKSFGSPNRAYTHQVVTRWYRAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLPGDSDLDQLTRIFETLGTPTEEQWPDMCSLPDYVTFKSFPGIPLQHIFIAAGDDLLELIQGLFLFNPCTRITASQALRTKYFSNRPGPTPGCQLPRPNCPVEALKEQSNPAMATKRKRAEALEQGILPKKLIF"

     misc_feature    137..1030
                     /gene="Cdk7"
                     /gene_synonym="CAK; P39 Mo15"
                     /note="Catalytic domain of the Serine/Threonine Kinase,
                     Cyclin-Dependent protein Kinase 7; Region: STKc_CDK7;
                     cd07841"
                     /db_xref="CDD:270833"
     misc_feature    order(158..169,173..178,182..184,221..223,227..229,
                     287..289,329..331,377..388,395..397,401..406,515..517,
                     521..523,527..532,536..538,569..571,578..580,584..586,
                     614..616,620..631,635..637,749..754)
                     /gene="Cdk7"
                     /gene_synonym="CAK; P39 Mo15"
                     /note="active site"
                     /db_xref="CDD:270833"
     misc_feature    order(158..160,164..178,182..184,221..223,227..229,
                     329..331,377..388,527..532,584..586)
                     /gene="Cdk7"
                     /gene_synonym="CAK; P39 Mo15"
                     /note="ATP binding site [chemical binding]; other site"
                     /db_xref="CDD:270833"
     misc_feature    order(263..271,275..277,284..289,293..298,305..310,
                     344..346,350..352,365..367,482..484,491..502,584..586,
                     590..601,611..616,947..949,959..967)
                     /gene="Cdk7"
                     /gene_synonym="CAK; P39 Mo15"
                     /note="CDK/cyclin interface [polypeptide binding]; other
                     site"
                     /db_xref="CDD:270833"
     misc_feature    order(287..289,401..403,515..517,521..523,578..580,
                     614..616,620..631,635..637,749..754)
                     /gene="Cdk7"
                     /gene_synonym="CAK; P39 Mo15"
                     /note="polypeptide substrate binding site [polypeptide
                     binding]; other site"
                     /db_xref="CDD:270833"
     misc_feature    order(566..601,605..637)
                     /gene="Cdk7"
                     /gene_synonym="CAK; P39 Mo15"
                     /note="activation loop (A-loop); other site"
                     /db_xref="CDD:270833"
     exon            173..232
                     /gene="Cdk7"
                     /gene_synonym="CAK; P39 Mo15"
                     /inference="alignment:Splign:2.1.0"
     exon            233..266
                     /gene="Cdk7"
                     /gene_synonym="CAK; P39 Mo15"
                     /inference="alignment:Splign:2.1.0"
     exon            267..334
                     /gene="Cdk7"
                     /gene_synonym="CAK; P39 Mo15"
                     /inference="alignment:Splign:2.1.0"
     exon            335..403
                     /gene="Cdk7"
                     /gene_synonym="CAK; P39 Mo15"
                     /inference="alignment:Splign:2.1.0"
     exon            404..514
                     /gene="Cdk7"
                     /gene_synonym="CAK; P39 Mo15"
                     /inference="alignment:Splign:2.1.0"
     exon            515..633
                     /gene="Cdk7"
                     /gene_synonym="CAK; P39 Mo15"
                     /inference="alignment:Splign:2.1.0"
     exon            634..733
                     /gene="Cdk7"
                     /gene_synonym="CAK; P39 Mo15"
                     /inference="alignment:Splign:2.1.0"
     exon            734..820
                     /gene="Cdk7"
                     /gene_synonym="CAK; P39 Mo15"
                     /inference="alignment:Splign:2.1.0"
     exon            821..970
                     /gene="Cdk7"
                     /gene_synonym="CAK; P39 Mo15"
                     /inference="alignment:Splign:2.1.0"
     exon            971..1118
                     /gene="Cdk7"
                     /gene_synonym="CAK; P39 Mo15"
                     /inference="alignment:Splign:2.1.0"
     exon            1119..1314
                     /gene="Cdk7"
                     /gene_synonym="CAK; P39 Mo15"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

atgcgcgtccagtgaacggaagtagctgttggaaactttcagacgctttaaattcctgcggggtggagggcttagtttagctgctggacgctggcttctcactcgtatggctgtggacgtgaaatctcgagcgaagcgctatgagaaactggacttcctcggagagggacagtttgctactgtctataaggccagagataagaacaccaaccagatcgtcgccattaagaaaatcaaacttggacacaggtcagaagctaaagatggtataaatagaacagccttaagggagataaagctcttgcaggaactaagtcatccaaatataattggtctccttgatgcatttggacataaatcgaacattagccttgtctttgattttatggagactgacctagaggttatcataaaggataacagtctcgtgttgaccccatcccacattaaagcctacatgctgatgactcttcagggcttggaatatttacatcagcactggattctacacagggatctgaaaccaaacaacttgttgttagatgagaatggagttctgaaactggcagattttggcctggccaaatcatttgggagccccaatagggcttacacacatcaagttgtgaccaggtggtaccgggcccccgagttactgtttggagctaggatgtacggtgtgggagtggacatgtgggctgtcggttgtatcttagcagaattgcttctaagggttccttttttgcctggagattcagaccttgatcagctaacaagaatatttgaaactctgggtacaccaaccgaagaacagtggcctgacatgtgtagtcttccagattacgtgacgttcaagagtttccctggcatccccctgcagcacatcttcattgcagctggagacgacctgcttgagctcatacaaggcttgttcttattcaacccatgtactagaattacagcttcacaggcgttgaggaccaagtacttcagtaatcgtccagggccaacacctggatgccagcttccaagaccaaactgtccagtggaagcattaaaggaacagtcaaatccagccatggcgacaaaacggaaaagagcggaggccttagaacaaggaatattgcccaagaagctaattttttagttgcagcgaacaatggacagtttcactgctgaaagaaatgatccaaaggcaaataacggaaaaaaaatagggaatattaaatactatataagaacttgtaaatactctacagatgtaaaatatgtaaagctatgggttatttttattaaatgtattttaaaataaaa

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