General information for g3003.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cyclin-dependent kinase 7.
Parent gene
- The parent gene g3003 is located on chr_3: 21915455..21918130 (- strand)
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.t1 | TTS | g3003.t1 | 21914225 | 21914225 |
| chr_3 | g3003 | g3003.t1 | isoform | g3003.t1 | 21914309 | 21915455 |
| chr_3 | g3003 | g3003.t1 | exon | g3003.t1.exon1 | 21914309 | 21914903 |
| chr_3 | g3003 | g3003.t1 | cds | g3003.t1.CDS1 | 21914309 | 21914903 |
| chr_3 | g3003 | g3003.t1 | exon | g3003.t1.exon2 | 21914968 | 21915341 |
| chr_3 | g3003 | g3003.t1 | cds | g3003.t1.CDS2 | 21914968 | 21915341 |
| chr_3 | g3003 | g3003.t1 | exon | g3003.t1.exon3 | 21915399 | 21915455 |
| chr_3 | g3003 | g3003.t1 | cds | g3003.t1.CDS3 | 21915399 | 21915455 |
| chr_3 | g3003 | g3003.t1 | TSS | g3003.t1 | 21915996 | 21915996 |
Sequences
>g3003.t1 Gene=g3003 Length=1026
ATGTCGAAATCATCATACAAAAAATATGAAAAGATATCATTTCTCGGCGAAGGTCAATTT
GCTATGGTATACAAAGCAAAAAATTTAGAAACAGGAGAAATTGTTGCTGTTAAAAAGATA
AAACTTGGCAGTAGAGAAGATGCAAGAGATGGAATAAATAGAACAGCATTGCGTGAGATA
AAACTACTTCAAGAGCTAAGTCATGAGAATGTTATTGGTCTACTGGATGTTTTCGGACAT
AAATCAAATGTATCATTAGTTTTTGAACTTGTTGATACTGACTTAGAAATTATTATCAAG
GATCAAAAGATAGTTTTAACACAAGCTAATATCAAATCGTATCTAATACAAACACTTAAA
GGACTTGAATATCTTCATCGTTCATGGATAATGCATAGAGACTTGAAACCTAATAATCTT
TTAATTTGCGCCAATGGTGTACTGAAAATAGCCGATTTTGGTTTGGCTAAATTCTATGCA
TCTCCAACGAGAATTAATACTCATCAAGTGGTAACAAGATGGTACCGTGCACCTGAACTT
TTATTCGGTAGTAGACATTATGCAACTGGAGTAGATATATGGGCTGTTGGATGTATTCTA
GCTGAACTCCTTTTGAGAGTGCCTTTTCTTCCTGGAGATTCTGACCTCAATCAACTTGAT
AAAATTTTCTCAGTATTTGGAACACCAAGTGAAGAAATATGGCCAGGCGTGAAATTGTTG
CCTGATTATATTCAATTTCGACCTTATCCAGCCATTCCATTAAAAGAAATTTTCACAGCA
TGTAGCGATGATCTGATTGATGTTGCAGATAAAATGTTTAGTCTCTATCCTTTGAAACGA
TGCACTGCATCTGAAGCTCTAAAAATGCCTTATTTTTCAAATCGTCCGCCGCCAACTGAA
GGATCAAAACTTCCAATGCCAACGAAACAACAAGAAGAAGAACCACCTTCTAAACCAAAT
CTCAAAAGAAAACTACTTGATCAAATCAATGATGCAGTTCCTGGTAAGAAGAGATTACAA
TTTTGA
>g3003.t1 Gene=g3003 Length=341
MSKSSYKKYEKISFLGEGQFAMVYKAKNLETGEIVAVKKIKLGSREDARDGINRTALREI
KLLQELSHENVIGLLDVFGHKSNVSLVFELVDTDLEIIIKDQKIVLTQANIKSYLIQTLK
GLEYLHRSWIMHRDLKPNNLLICANGVLKIADFGLAKFYASPTRINTHQVVTRWYRAPEL
LFGSRHYATGVDIWAVGCILAELLLRVPFLPGDSDLNQLDKIFSVFGTPSEEIWPGVKLL
PDYIQFRPYPAIPLKEIFTACSDDLIDVADKMFSLYPLKRCTASEALKMPYFSNRPPPTE
GSKLPMPTKQQEEEPPSKPNLKRKLLDQINDAVPGKKRLQF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g3003.t1 | CDD | cd07841 | STKc_CDK7 | 8 | 305 | 0.0 |
| 5 | g3003.t1 | Gene3D | G3DSA:3.30.200.20 | Phosphorylase Kinase; domain 1 | 1 | 92 | 6.2E-33 |
| 6 | g3003.t1 | Gene3D | G3DSA:1.10.510.10 | Transferase(Phosphotransferase) domain 1 | 93 | 308 | 1.7E-69 |
| 11 | g3003.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 292 | 327 | - |
| 2 | g3003.t1 | PANTHER | PTHR24056:SF375 | CYCLIN-DEPENDENT KINASE 7 | 4 | 310 | 5.9E-140 |
| 3 | g3003.t1 | PANTHER | PTHR24056 | CELL DIVISION PROTEIN KINASE | 4 | 310 | 5.9E-140 |
| 1 | g3003.t1 | Pfam | PF00069 | Protein kinase domain | 9 | 292 | 2.3E-71 |
| 9 | g3003.t1 | ProSitePatterns | PS00107 | Protein kinases ATP-binding region signature. | 15 | 39 | - |
| 8 | g3003.t1 | ProSitePatterns | PS00108 | Serine/Threonine protein kinases active-site signature. | 130 | 142 | - |
| 12 | g3003.t1 | ProSiteProfiles | PS50011 | Protein kinase domain profile. | 9 | 292 | 45.418 |
| 10 | g3003.t1 | SMART | SM00220 | serkin_6 | 9 | 292 | 1.4E-91 |
| 4 | g3003.t1 | SUPERFAMILY | SSF56112 | Protein kinase-like (PK-like) | 5 | 298 | 5.53E-94 |
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
- This transcript has been annotated with K02202 (cyclin-dependent kinase 7)
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.
