LOCUS       NM_001398656            1314 bp    mRNA    linear   ROD 24-SEP-2023
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 AR 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 JM 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 SY and Chiang CM.
  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 JT, Ge H, Gibbs E, Sancar A, Hurwitz J and Pan ZQ.
  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 MC, Smith JL and Masters JN.
  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 JP, Nigg EA 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 TP, Conaway JW, Conaway RC, Weinberg RA and
            Young RA.
  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
            JACYVU010000065.1.
            
            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 :: SRR8487231.52780.1,
                                           SRR8487227.292185.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA5760383, SAMEA5760389
                                           [ECO:0000348]
            ##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               JACYVU010000065.1  24370521-24370692   c
            173-232             JACYVU010000065.1  24370200-24370259   c
            233-266             JACYVU010000065.1  24364425-24364458   c
            267-334             JACYVU010000065.1  24363058-24363125   c
            335-403             JACYVU010000065.1  24361010-24361078   c
            404-514             JACYVU010000065.1  24357799-24357909   c
            515-633             JACYVU010000065.1  24356730-24356848   c
            634-733             JACYVU010000065.1  24353969-24354068   c
            734-820             JACYVU010000065.1  24352329-24352415   c
            821-970             JACYVU010000065.1  24348683-24348832   c
            971-1118            JACYVU010000065.1  24346920-24347067   c
            1119-1314           JACYVU010000065.1  24345828-24346023   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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