Gene loci information

Transcript annotation

  • This transcript has been annotated as Tyrosine-protein kinase Shark.

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
HiC_scaffold_384 g17821 g17821.t1 isoform g17821.t1 114 2706
HiC_scaffold_384 g17821 g17821.t1 exon g17821.t1.exon1 114 432
HiC_scaffold_384 g17821 g17821.t1 cds g17821.t1.CDS1 114 432
HiC_scaffold_384 g17821 g17821.t1 exon g17821.t1.exon2 504 2278
HiC_scaffold_384 g17821 g17821.t1 cds g17821.t1.CDS2 504 2278
HiC_scaffold_384 g17821 g17821.t1 exon g17821.t1.exon3 2368 2546
HiC_scaffold_384 g17821 g17821.t1 cds g17821.t1.CDS3 2368 2546
HiC_scaffold_384 g17821 g17821.t1 exon g17821.t1.exon4 2631 2706
HiC_scaffold_384 g17821 g17821.t1 cds g17821.t1.CDS4 2631 2706
HiC_scaffold_384 g17821 g17821.t1 TSS g17821.t1 2801 2801
HiC_scaffold_384 g17821 g17821.t1 TTS g17821.t1 18774 18774

Sequences

>g17821.t1 Gene=g17821 Length=2349
ATGAGTCGAGATGAAAGTCTAGACTGGTTTCATGGTAGAATTTCGCGATTAGAGGCAGAG
AAAATTCTTCTTGAAGAATCTCAAAAACTTGATATCTCCGACAGTATTTTTCTTGTTCGT
GAAAGTTCAACATTGATTAATAACTATGTAAGTATCCGTTATAATCGAAATGAATTTTTT
CATTATCAAATACAAAGACATGGAGATGATTCATTCTTCTCCATTGACTCTCAATTCATT
CATCACGATTGGACGCACAATGAATCGAATCTCTGTACAAAATTAGGAAAGTTTGTAAAG
AAAGGTCCACCACCATTAAAATATTGCAAATTAGGAAAAGCAAATTTGCTTCATCGTGCC
ACAAAGCATAATAATTTAAATGTTGTCAAAGAAATTTTATCGACATCATATCGAAATTTA
GATGCAAAAGATGAAAATGGAATGACAGCAGTTCATTTAGCTGCAATAAATAAAGTCAGT
GCTGAAATTATGAAATTGCTCATGAAAAATGGAAGTGCCTTAGCAAGTAGAGACTCAGTT
GGAAATACACCACTGCATTATGCTTGTAAATTTGAATGCAAAGAAATGGTTGAACTTTTA
ATTGGTGCAAGTAAACCATTGATTTATGCTAGAAACACTTTTACACACGAAGTGCCATTA
CATGAAGCTGCCAAAGTTGGAAATCTTGAAATTGTCAAAATTTTACTGCAAAATAATGCA
GCAAGTATGCCGAGAGCTAATAATGGAAAACTTCCAATCAATTATGCAAGAGAGAAAGGG
CATTATGATGTTGTTGAATATTTGGAAAAATATGTGCCAGTTTGTAATACATTTAGCCAT
AAGTGGCATCATGGAACATTAGATAGAGAAGGGGCAAGAACTTTGTTATTGAAGAAAAGA
AATGAACTTTATGAAAAATATCGTGAAGAATATGCATTGGAAGAGAATGTCTATGTTAAT
GATAATAAAGAAATTAATGATTTAATTTGTGGATTGTTCTTGGTAAGAACAAGTGAAAGA
AATGGTGGATTAGATGTCATAACTATGCTTCATGATGACGATGACCTAAATATTAGAAAT
TATGTAATTCATAAATCTGACAATTTAAAATATTTTTTATACGATGATGGACCATTTTTC
ACTTCATTAGAACATCTTATAAGCTATTACATGACTCATGCTGATGGGCTTCCGGCTAAA
TTAACACAATTTGTGTCTCCAATCGTTCGTCCACCAATTCCAACTTTACAGAAAAAGTCA
AAATCTGTGATGCAATCTCCAGTTGTTAGTACAAATTCAATATCATCACCTGAAAGTGCT
AACAATTCAATGACAATAGAGTCTCAAACAAAAGCAAAATCATCAGTTTTCACTTTATTC
AAGAAAAAAAAGCATTCCCTTCCAACTTCACTCTCTAAAGAAGACAAACCATCAGTTGAT
TTGTCAATGGATTCTTTCAATAAATCATTGTCATTTTCAACGAATTTTCTTACAAATTAT
GGCGTTCCTCCGACATCAAAGAGGCCATCAACACAAGAAGATCAATTTACAGAAAGCGAT
CAATTTTTGATCAACAATCAGACAGTTCAAGACTCAAAACCACAAGAAATGATTTATTTC
ATGGATCCACCAAAAAGGAATAAAATAGAATGGAATCAACTTGATCCGGAATTGTATGAA
ACGCAAAAGAACTTTTTAAAAGAAATTACTCGAAGTTCTGGTGCAAATTATTATGTCTCA
AAAGATGATCTACATTTTGACAATGAAATTGGTTCAGGAGAATTTGGAAATGTCTTAAGG
GGAATTTTTAAATTATCAAATGGCAAGAAAATTTGGGTTGCAATAAAAACTTTACATGAG
AGGCATTATGAAGAAAATCTTCCAGAATTTTTAAAAGAAGCTTCAGTTATGATAAAATTA
GACAATTCCTATGTCGTAAAACTAATTGTTCAAGAGCTCTGTAGTTTTGGATCACTCGCT
GAATATTTAGTAGAAAACAAAGATGATATCGATTATAAATTAATTGACTTCTCGCAATAT
TTACTCGTCTCGAAGCAACATTGCAAAATATCTAACTTTGGTCTCTCACGTGCCATTGGA
ATCGATAAAGATTTCTATCAATCAAGTACTGGTGGACGCTGGCCATTAAAATGGTATGCG
CCTGAATCTTTCTGTGGAAAATTTTCTCATTCAAGTGATGTGTGGAGTTTCGGTATAACT
TTGTGGGAAATTTATTCAAAAAGTGATGTACCCTATGATGATTTGTCTGGAAGTGAAGTC
AATGAATTAATTGAGAAAGGTCAGCGTCTTGCAAGACCAGAAGGTTGTCCATCCAGAAGA
TGTGTATAG

>g17821.t1 Gene=g17821 Length=782
MSRDESLDWFHGRISRLEAEKILLEESQKLDISDSIFLVRESSTLINNYVSIRYNRNEFF
HYQIQRHGDDSFFSIDSQFIHHDWTHNESNLCTKLGKFVKKGPPPLKYCKLGKANLLHRA
TKHNNLNVVKEILSTSYRNLDAKDENGMTAVHLAAINKVSAEIMKLLMKNGSALASRDSV
GNTPLHYACKFECKEMVELLIGASKPLIYARNTFTHEVPLHEAAKVGNLEIVKILLQNNA
ASMPRANNGKLPINYAREKGHYDVVEYLEKYVPVCNTFSHKWHHGTLDREGARTLLLKKR
NELYEKYREEYALEENVYVNDNKEINDLICGLFLVRTSERNGGLDVITMLHDDDDLNIRN
YVIHKSDNLKYFLYDDGPFFTSLEHLISYYMTHADGLPAKLTQFVSPIVRPPIPTLQKKS
KSVMQSPVVSTNSISSPESANNSMTIESQTKAKSSVFTLFKKKKHSLPTSLSKEDKPSVD
LSMDSFNKSLSFSTNFLTNYGVPPTSKRPSTQEDQFTESDQFLINNQTVQDSKPQEMIYF
MDPPKRNKIEWNQLDPELYETQKNFLKEITRSSGANYYVSKDDLHFDNEIGSGEFGNVLR
GIFKLSNGKKIWVAIKTLHERHYEENLPEFLKEASVMIKLDNSYVVKLIVQELCSFGSLA
EYLVENKDDIDYKLIDFSQYLLVSKQHCKISNFGLSRAIGIDKDFYQSSTGGRWPLKWYA
PESFCGKFSHSSDVWSFGITLWEIYSKSDVPYDDLSGSEVNELIEKGQRLARPEGCPSRR
CV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g17821.t1 Gene3D G3DSA:3.30.505.10 SHC Adaptor Protein 1 97 4.1E-12
19 g17821.t1 Gene3D G3DSA:1.25.40.20 - 98 270 3.1E-36
22 g17821.t1 Gene3D G3DSA:3.30.505.10 SHC Adaptor Protein 271 406 2.4E-21
20 g17821.t1 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 541 655 1.2E-17
21 g17821.t1 Gene3D G3DSA:1.10.510.10 Transferase(Phosphotransferase) domain 1 674 781 6.8E-24
7 g17821.t1 PANTHER PTHR24418 TYROSINE-PROTEIN KINASE 3 673 2.4E-107
9 g17821.t1 PANTHER PTHR24418:SF372 TYROSINE-PROTEIN KINASE SHARK 3 673 2.4E-107
8 g17821.t1 PANTHER PTHR24418 TYROSINE-PROTEIN KINASE 681 778 2.4E-107
10 g17821.t1 PANTHER PTHR24418:SF372 TYROSINE-PROTEIN KINASE SHARK 681 778 2.4E-107
14 g17821.t1 PRINTS PR00401 SH2 domain signature 9 23 5.8E-9
13 g17821.t1 PRINTS PR00401 SH2 domain signature 34 44 5.8E-9
11 g17821.t1 PRINTS PR00401 SH2 domain signature 357 367 5.8E-9
12 g17821.t1 PRINTS PR00401 SH2 domain signature 379 393 5.8E-9
1 g17821.t1 Pfam PF00017 SH2 domain 9 77 3.9E-9
4 g17821.t1 Pfam PF12796 Ankyrin repeats (3 copies) 117 203 2.8E-14
3 g17821.t1 Pfam PF12796 Ankyrin repeats (3 copies) 217 268 1.3E-7
2 g17821.t1 Pfam PF00017 SH2 domain 331 390 2.2E-7
5 g17821.t1 Pfam PF07714 Protein tyrosine and serine/threonine kinase 584 671 2.6E-12
6 g17821.t1 Pfam PF07714 Protein tyrosine and serine/threonine kinase 681 778 1.5E-27
24 g17821.t1 ProSitePatterns PS00107 Protein kinases ATP-binding region signature. 590 616 -
36 g17821.t1 ProSiteProfiles PS50001 Src homology 2 (SH2) domain profile. 9 73 12.925
32 g17821.t1 ProSiteProfiles PS50297 Ankyrin repeat region circular profile. 112 268 33.898
34 g17821.t1 ProSiteProfiles PS50088 Ankyrin repeat profile. 146 179 10.339
33 g17821.t1 ProSiteProfiles PS50088 Ankyrin repeat profile. 215 240 9.805
35 g17821.t1 ProSiteProfiles PS50001 Src homology 2 (SH2) domain profile. 282 408 16.944
37 g17821.t1 ProSiteProfiles PS50011 Protein kinase domain profile. 584 782 12.429
31 g17821.t1 SMART SM00252 SH2_5 7 89 9.3E-6
27 g17821.t1 SMART SM00248 ANK_2a 112 142 9.9
26 g17821.t1 SMART SM00248 ANK_2a 146 176 0.071
29 g17821.t1 SMART SM00248 ANK_2a 180 210 0.055
28 g17821.t1 SMART SM00248 ANK_2a 215 245 0.06
25 g17821.t1 SMART SM00248 ANK_2a 248 277 57.0
30 g17821.t1 SMART SM00252 SH2_5 280 396 8.7E-12
18 g17821.t1 SUPERFAMILY SSF55550 SH2 domain 6 101 4.04E-13
15 g17821.t1 SUPERFAMILY SSF48403 Ankyrin repeat 110 270 9.78E-34
17 g17821.t1 SUPERFAMILY SSF55550 SH2 domain 272 406 1.18E-17
16 g17821.t1 SUPERFAMILY SSF56112 Protein kinase-like (PK-like) 575 778 1.63E-36

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:0005524 ATP binding MF
GO:0005515 protein 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