Gene loci information

Transcript annotation

  • This transcript has been annotated as Cyclin-dependent kinase 7.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_3 g3003 g3003.t14 TTS g3003.t14 21914225 21914225
chr_3 g3003 g3003.t14 isoform g3003.t14 21914309 21915455
chr_3 g3003 g3003.t14 exon g3003.t14.exon1 21914309 21914903
chr_3 g3003 g3003.t14 cds g3003.t14.CDS1 21914309 21914903
chr_3 g3003 g3003.t14 exon g3003.t14.exon2 21914968 21915455
chr_3 g3003 g3003.t14 cds g3003.t14.CDS2 21914968 21915335
chr_3 g3003 g3003.t14 TSS g3003.t14 21915996 21915996

Sequences

>g3003.t14 Gene=g3003 Length=1083
ATGTCGAAATCATCATACAAAAAATATGAAAAGATATCATTTCTCGGCGAAGGTCAAGTA
AGTTTTGTTGTACTTTAATAATTATTTCACACGCTCAATAATGTGCCGCTTTAGTTTGCT
ATGGTATACAAAGCAAAAAATTTAGAAACAGGAGAAATTGTTGCTGTTAAAAAGATAAAA
CTTGGCAGTAGAGAAGATGCAAGAGATGGAATAAATAGAACAGCATTGCGTGAGATAAAA
CTACTTCAAGAGCTAAGTCATGAGAATGTTATTGGTCTACTGGATGTTTTCGGACATAAA
TCAAATGTATCATTAGTTTTTGAACTTGTTGATACTGACTTAGAAATTATTATCAAGGAT
CAAAAGATAGTTTTAACACAAGCTAATATCAAATCGTATCTAATACAAACACTTAAAGGA
CTTGAATATCTTCATCGTTCATGGATAATGCATAGAGACTTGAAACCTAATAATCTTTTA
ATTTGCGCCAATGGTGTACTGAAAATAGCCGATTTTGGTTTGGCTAAATTCTATGCATCT
CCAACGAGAATTAATACTCATCAAGTGGTAACAAGATGGTACCGTGCACCTGAACTTTTA
TTCGGTAGTAGACATTATGCAACTGGAGTAGATATATGGGCTGTTGGATGTATTCTAGCT
GAACTCCTTTTGAGAGTGCCTTTTCTTCCTGGAGATTCTGACCTCAATCAACTTGATAAA
ATTTTCTCAGTATTTGGAACACCAAGTGAAGAAATATGGCCAGGCGTGAAATTGTTGCCT
GATTATATTCAATTTCGACCTTATCCAGCCATTCCATTAAAAGAAATTTTCACAGCATGT
AGCGATGATCTGATTGATGTTGCAGATAAAATGTTTAGTCTCTATCCTTTGAAACGATGC
ACTGCATCTGAAGCTCTAAAAATGCCTTATTTTTCAAATCGTCCGCCGCCAACTGAAGGA
TCAAAACTTCCAATGCCAACGAAACAACAAGAAGAAGAACCACCTTCTAAACCAAATCTC
AAAAGAAAACTACTTGATCAAATCAATGATGCAGTTCCTGGTAAGAAGAGATTACAATTT
TGA

>g3003.t14 Gene=g3003 Length=320
MVYKAKNLETGEIVAVKKIKLGSREDARDGINRTALREIKLLQELSHENVIGLLDVFGHK
SNVSLVFELVDTDLEIIIKDQKIVLTQANIKSYLIQTLKGLEYLHRSWIMHRDLKPNNLL
ICANGVLKIADFGLAKFYASPTRINTHQVVTRWYRAPELLFGSRHYATGVDIWAVGCILA
ELLLRVPFLPGDSDLNQLDKIFSVFGTPSEEIWPGVKLLPDYIQFRPYPAIPLKEIFTAC
SDDLIDVADKMFSLYPLKRCTASEALKMPYFSNRPPPTEGSKLPMPTKQQEEEPPSKPNL
KRKLLDQINDAVPGKKRLQF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g3003.t14 CDD cd07841 STKc_CDK7 2 284 0.0
5 g3003.t14 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 1 71 1.6E-24
6 g3003.t14 Gene3D G3DSA:1.10.510.10 Transferase(Phosphotransferase) domain 1 72 287 1.4E-69
10 g3003.t14 MobiDBLite mobidb-lite consensus disorder prediction 271 306 -
2 g3003.t14 PANTHER PTHR24056:SF375 CYCLIN-DEPENDENT KINASE 7 2 289 6.0E-130
3 g3003.t14 PANTHER PTHR24056 CELL DIVISION PROTEIN KINASE 2 289 6.0E-130
1 g3003.t14 Pfam PF00069 Protein kinase domain 2 271 2.7E-66
8 g3003.t14 ProSitePatterns PS00108 Serine/Threonine protein kinases active-site signature. 109 121 -
11 g3003.t14 ProSiteProfiles PS50011 Protein kinase domain profile. 1 271 41.799
9 g3003.t14 SMART SM00220 serkin_6 2 271 3.0E-77
4 g3003.t14 SUPERFAMILY SSF56112 Protein kinase-like (PK-like) 2 277 1.23E-86

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0008353 RNA polymerase II CTD heptapeptide repeat kinase activity MF
GO:0005675 transcription factor TFIIH holo complex CC
GO:0070985 transcription factor TFIIK complex CC
GO:0005524 ATP binding MF
GO:0004672 protein kinase activity MF
GO:0006468 protein phosphorylation BP

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values