General information for g698.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Tyrosine-protein kinase CSK.
Parent gene
- The parent gene g698 is located on chr_3: 5409462..5410346 (- 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 | g698 | g698.t1 | TTS | g698.t1 | 5407135 | 5407135 |
| chr_3 | g698 | g698.t1 | isoform | g698.t1 | 5407823 | 5410192 |
| chr_3 | g698 | g698.t1 | exon | g698.t1.exon1 | 5407823 | 5408086 |
| chr_3 | g698 | g698.t1 | cds | g698.t1.CDS1 | 5407823 | 5408086 |
| chr_3 | g698 | g698.t1 | exon | g698.t1.exon2 | 5408147 | 5408279 |
| chr_3 | g698 | g698.t1 | cds | g698.t1.CDS2 | 5408147 | 5408279 |
| chr_3 | g698 | g698.t1 | exon | g698.t1.exon3 | 5408495 | 5408560 |
| chr_3 | g698 | g698.t1 | cds | g698.t1.CDS3 | 5408495 | 5408560 |
| chr_3 | g698 | g698.t1 | exon | g698.t1.exon4 | 5408627 | 5408788 |
| chr_3 | g698 | g698.t1 | cds | g698.t1.CDS4 | 5408627 | 5408788 |
| chr_3 | g698 | g698.t1 | exon | g698.t1.exon5 | 5408884 | 5409390 |
| chr_3 | g698 | g698.t1 | cds | g698.t1.CDS5 | 5408884 | 5409390 |
| chr_3 | g698 | g698.t1 | exon | g698.t1.exon6 | 5409462 | 5410192 |
| chr_3 | g698 | g698.t1 | cds | g698.t1.CDS6 | 5409462 | 5410192 |
| chr_3 | g698 | g698.t1 | TSS | g698.t1 | 5410934 | 5410934 |
Sequences
>g698.t1 Gene=g698 Length=1863
ATGAATATAAACACAACATTACAAACAAGTCATCATCATCATCACCATCATCATCAGCAA
CATCATCAAACCTCTCCTAATACCAATTCATTATCTAATCAACAACAATATCATACTAAC
TCTTCTGTAATAATACATCAAGGTCAACAACATCAACAGAAGGCTGTTGTCAATCATAAT
CCGAGTGTAGAGCGCTTCCAAGCACTTGATGATCCATGGTTAAAACAAAATACTACTACT
GCTCAACAAGGACCAACTCCTCCACTTAGACAACATAAACGACTTGGTCCAAGCACAAGT
CATCATTCATCAACAACATCGTCTGCCACTATTGCTGCTGCAGCAACTACTTCTTCCATA
TCGCAAATTAAAAAACCAATTACATTGGCCAATAGCACTTATAATCAACCTGTTTATTTG
TCAACACAAACACAAACAACACCTGGATTACAAGCGCCTCAAAATTTATTGACTTCACAA
ATATCGCCCAAATCGCCAATTCAAAATTTTCCAGGCAGTGGCGGTAGTGCCATAACGCAC
AATATGATGTCCTCATCATCCTTGAGTAATAGTGGCAATTCAAAGTCACAACATTTGCAT
AGTGGTGCATTAAGCAATAATAATAACAACAATAGCATTTATGATGACTTAAATCTTAAT
ACAAATGGACCGATATCGCATACAACATCGACACATCAAAGAAAACTCGAAATGAAATTA
AATTCCACACCATGGTTCTATGGTAAAATTACAAGAGATGAAGCTGAACGTTTATTACAT
CCGCGTGAAGAAGGATTATTTTTAGTTAGAGAATCAACAAATTATCCGGGCGATTACACG
CTATGTGTTTGTTTCCAGGAGAAAGTAGAACATTATCGTGTCAAATATCTAGACAAGAAG
CTTACAATTGATGATGAAGAGTACTTTGATGATCTAAGTCAACTTGTTGCCCATTATGAA
GAAGATGCCGATGGATTATGTACACAGCTCAAAAAGCCTTTGGAGAAAAATTTAAATCAT
CATCATAATCAGGGGCTATCATGCATGAAATCTACAGATTTTATTGAGCAAGGTTGGGTA
ATTCCAGAACAAGATTTGCATCTGAAAGAGAGCATTGGAAAAGGTGAATTTGGTGATGTA
ATGCTAGGGTACTTAAAAGGCGAGAAAGTTGCCGTTAAAATGCTTAAAGATTCAACAGCA
GCAGCACAGAAATTTTTAGCAGAAGCATCTGTAATGACAACATTAGAGCACGAGAATCTT
GTGAAATTCATTGGAATAGTCTTCAATAAACAACATCTTTATCTTGTCACTGAATATATG
AGTAAAGGATCATTAGTCGATTATTTAAGATCACGAGGTCGTCAACACATTACCAGAAAG
GATCAAATCAATTTTGCAAGTGACACATGTTCTGGTATGGAATATTTAGAAGCAAAGAAA
GTTGTGCATCGTGACTTAGCTGCAAGAAATGTACTTATTTCCGAAGAGTGTGTGGCAAAA
GTGGCTGATTTTGGTTTAGCGCGTGAGGAGTGTATGAACAGCAATGATATAGGAAAACTT
CCAATCAAATGGTCAGCACCAGAAGCTCTTAAAAGTGGCCAATTTTCAAACAAGTCAGAC
ATTTGGAGTTTTGGAATTCTATTATGGGAAATTTATTCTTTCGGACGTGTTCCTTATCCT
CGTATTCCACTTGCAGATGTTACAAAACATGTTGAGGCCGGTTATAAAATGGAAGCACCT
GAAGGTTGTCCCACAGAAATCTACGATATGATGAAAGAATGCTGGGACCTTAATCCAAAA
AATCGTCCAACATTTAGAGACCTTGCGATAAGATTAAAACATTTAAAAACGATAACTACA
TAA
>g698.t1 Gene=g698 Length=620
MNINTTLQTSHHHHHHHHQQHHQTSPNTNSLSNQQQYHTNSSVIIHQGQQHQQKAVVNHN
PSVERFQALDDPWLKQNTTTAQQGPTPPLRQHKRLGPSTSHHSSTTSSATIAAAATTSSI
SQIKKPITLANSTYNQPVYLSTQTQTTPGLQAPQNLLTSQISPKSPIQNFPGSGGSAITH
NMMSSSSLSNSGNSKSQHLHSGALSNNNNNNSIYDDLNLNTNGPISHTTSTHQRKLEMKL
NSTPWFYGKITRDEAERLLHPREEGLFLVRESTNYPGDYTLCVCFQEKVEHYRVKYLDKK
LTIDDEEYFDDLSQLVAHYEEDADGLCTQLKKPLEKNLNHHHNQGLSCMKSTDFIEQGWV
IPEQDLHLKESIGKGEFGDVMLGYLKGEKVAVKMLKDSTAAAQKFLAEASVMTTLEHENL
VKFIGIVFNKQHLYLVTEYMSKGSLVDYLRSRGRQHITRKDQINFASDTCSGMEYLEAKK
VVHRDLAARNVLISEECVAKVADFGLAREECMNSNDIGKLPIKWSAPEALKSGQFSNKSD
IWSFGILLWEIYSFGRVPYPRIPLADVTKHVEAGYKMEAPEGCPTEIYDMMKECWDLNPK
NRPTFRDLAIRLKHLKTITT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 22 | g698.t1 | CDD | cd09937 | SH2_csk_like | 244 | 336 | 1.70644E-59 |
| 23 | g698.t1 | CDD | cd05039 | PTKc_Csk_like | 359 | 615 | 2.34999E-180 |
| 18 | g698.t1 | Gene3D | G3DSA:3.30.505.10 | SHC Adaptor Protein | 223 | 348 | 3.0E-34 |
| 17 | g698.t1 | Gene3D | G3DSA:1.10.510.10 | Transferase(Phosphotransferase) domain 1 | 359 | 619 | 1.5E-85 |
| 29 | g698.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 35 | - |
| 28 | g698.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 78 | 111 | - |
| 3 | g698.t1 | PANTHER | PTHR24418 | TYROSINE-PROTEIN KINASE | 235 | 617 | 6.4E-155 |
| 4 | g698.t1 | PANTHER | PTHR24418:SF407 | TYROSINE-PROTEIN KINASE CSK | 235 | 617 | 6.4E-155 |
| 21 | g698.t1 | PIRSF | PIRSF000615 | TyrPK_CSF1-R | 3 | 67 | 320.0 |
| 20 | g698.t1 | PIRSF | PIRSF000615 | TyrPK_CSF1-R | 355 | 460 | 7.2E-12 |
| 19 | g698.t1 | PIRSF | PIRSF000615 | TyrPK_CSF1-R | 453 | 619 | 3.4E-58 |
| 9 | g698.t1 | PRINTS | PR00401 | SH2 domain signature | 245 | 259 | 6.8E-16 |
| 6 | g698.t1 | PRINTS | PR00401 | SH2 domain signature | 264 | 274 | 6.8E-16 |
| 8 | g698.t1 | PRINTS | PR00401 | SH2 domain signature | 276 | 287 | 6.8E-16 |
| 7 | g698.t1 | PRINTS | PR00401 | SH2 domain signature | 288 | 298 | 6.8E-16 |
| 5 | g698.t1 | PRINTS | PR00401 | SH2 domain signature | 308 | 322 | 6.8E-16 |
| 11 | g698.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 437 | 450 | 7.6E-38 |
| 13 | g698.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 475 | 493 | 7.6E-38 |
| 12 | g698.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 520 | 530 | 7.6E-38 |
| 14 | g698.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 539 | 561 | 7.6E-38 |
| 10 | g698.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 583 | 605 | 7.6E-38 |
| 1 | g698.t1 | Pfam | PF00017 | SH2 domain | 245 | 319 | 2.7E-24 |
| 2 | g698.t1 | Pfam | PF07714 | Protein tyrosine and serine/threonine kinase | 366 | 609 | 1.3E-90 |
| 27 | g698.t1 | ProSitePatterns | PS00107 | Protein kinases ATP-binding region signature. | 372 | 393 | - |
| 26 | g698.t1 | ProSitePatterns | PS00109 | Tyrosine protein kinases specific active-site signature. | 481 | 493 | - |
| 30 | g698.t1 | ProSiteProfiles | PS50001 | Src homology 2 (SH2) domain profile. | 245 | 334 | 24.478 |
| 31 | g698.t1 | ProSiteProfiles | PS50011 | Protein kinase domain profile. | 366 | 617 | 42.124 |
| 25 | g698.t1 | SMART | SM00252 | SH2_5 | 243 | 325 | 3.9E-32 |
| 24 | g698.t1 | SMART | SM00219 | tyrkin_6 | 366 | 612 | 2.9E-124 |
| 16 | g698.t1 | SUPERFAMILY | SSF55550 | SH2 domain | 240 | 385 | 2.42E-35 |
| 15 | g698.t1 | SUPERFAMILY | SSF56112 | Protein kinase-like (PK-like) | 346 | 608 | 4.05E-77 |
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:0004713 | protein tyrosine kinase activity | MF |
| GO:0005524 | ATP binding | MF |
| GO:0004672 | protein kinase activity | MF |
| GO:0006468 | protein phosphorylation | BP |
KEGG
Orthology
- This transcript has been annotated with K05728 (c-src tyrosine kinase)
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.
