Gene loci information

Transcript annotation

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

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 g3711 g3711.t2 TTS g3711.t2 27578150 27578150
chr_3 g3711 g3711.t2 isoform g3711.t2 27578196 27583675
chr_3 g3711 g3711.t2 exon g3711.t2.exon1 27578196 27578515
chr_3 g3711 g3711.t2 cds g3711.t2.CDS1 27578196 27578515
chr_3 g3711 g3711.t2 exon g3711.t2.exon2 27578581 27578652
chr_3 g3711 g3711.t2 cds g3711.t2.CDS2 27578581 27578652
chr_3 g3711 g3711.t2 exon g3711.t2.exon3 27578866 27579400
chr_3 g3711 g3711.t2 cds g3711.t2.CDS3 27578866 27579400
chr_3 g3711 g3711.t2 exon g3711.t2.exon4 27579462 27579659
chr_3 g3711 g3711.t2 cds g3711.t2.CDS4 27579462 27579659
chr_3 g3711 g3711.t2 exon g3711.t2.exon5 27580298 27580457
chr_3 g3711 g3711.t2 cds g3711.t2.CDS5 27580298 27580457
chr_3 g3711 g3711.t2 exon g3711.t2.exon6 27580516 27580929
chr_3 g3711 g3711.t2 cds g3711.t2.CDS6 27580516 27580929
chr_3 g3711 g3711.t2 exon g3711.t2.exon7 27580996 27581191
chr_3 g3711 g3711.t2 cds g3711.t2.CDS7 27580996 27581191
chr_3 g3711 g3711.t2 exon g3711.t2.exon8 27581246 27581342
chr_3 g3711 g3711.t2 cds g3711.t2.CDS8 27581246 27581342
chr_3 g3711 g3711.t2 exon g3711.t2.exon9 27581458 27581648
chr_3 g3711 g3711.t2 cds g3711.t2.CDS9 27581458 27581648
chr_3 g3711 g3711.t2 exon g3711.t2.exon10 27583486 27583675
chr_3 g3711 g3711.t2 cds g3711.t2.CDS10 27583486 27583675
chr_3 g3711 g3711.t2 TSS g3711.t2 27584122 27584122

Sequences

>g3711.t2 Gene=g3711 Length=2373
ATGGGACTCTCAACACAGGGAAAGAACATTCACGATGTAATAACTGCACGACATGAGTCC
GAAATTCGTCTCATCGAAGTTATGCGTAAATGTTTATTACTAAAAGTAAAGTGCGATCGT
GATTATGCGTCTTCAATCCAGAGTGTTTCCGTCGTTGGTCTCAAAATTGATCGAATAGAC
GATCTAAATGGAAGTCAAATTTTCAAAACATGGAAGCGATTTATGGAAGAATTAGAAAAT
CAATCTAAGTTGATTCGCAAGAAAATGGAATGTTTAGAGAACATTTGCATCGATCGAATA
TCAAATATTTTAGTTGAAAAAAGAAAAATAAAGAAGCAATGTCAAGACGATCATGAAAAA
ATTGCGTCAAGACTATTCCAGTTTACCGATGAAGTTGCAAAAAAGAAGACTGAGTACAAT
AAGCAACTAGAATATTACAAACAAATGAGATTACGCTTCGAAGAACATTACATTAAATCT
GGTAGAGCAGGTCGGAAGTTAGATGATGTGAGAGAAAAGTACCAAAAGGCATGTAGAAAA
TTGCATTTGATTCACAATGAATATGTATTACTGTTACACGAAGCGACTGAAGTTGAAAAA
GATTATAGAACCGACCTCTTTCCTACTTTCTTATCAAATCAAGAAGCTCTCCATGAACAA
TTTAATGAAAATTGGAATAGTATATTAGTAGATATTGCAAAACTACTCGATCTATCATCA
GCTGATGAATTTTTGAAAACACAAGAACAATTAAGTAATGGTTTGAAGGGTTCAATATCA
AAAGATGAGTATAATGACATATTGGAAAAATATAAAGCATCACCGATAGTCTTTCATTTT
GATGAAAACTTAATAAATGACAATGTTGGAAAATTATTGCCTAATCAATTAGCTGTAGAT
AACTTAACAATCGATTGGCTAAAACAAAAAATGCTAGAGCTTGAACAATCAATGAAAGAA
TGCCAAGAAGAACAGCAAAAGCTCAAGCAAAGCAATAGCAGTGAACAGTTGACACTAAAT
AATTTACTCAACAAGAGTCTTGTGAATATTGAAGGTCAAAATCATAGTTCTCAAATAGTT
GATTTAAAATTAAAATCCTTAAAGAATGAAGAGCGCCAAATGTTTAAAGTACTGGAAATT
ATCAAATCATCGTTGAATGAAGTTTCATTAAATGAATTACCAAGTGGTTGTGATGATGAT
TTACCATCAGTTGTTGTTGAAAATGATGAGAAATATAGAAATAGTACTCTTACAGTTTCA
CCGACTCAGCCCTTATATCTTGAACCATGGTTTCATGGTGTGCTACCAAGAGAAGAAGTT
GTACGATTATTACGAAATGAAGGTGATTTTTTGGTACGCGAAACAACTAGAAACGATGAA
ACTCAAATTGTATTGAGTGTCTGTTGGAATGGACATAAACATTTTATTGTGCAAACGACT
GCTGATAACCATTATCGATTTGAAGGTCCATCATTTGCGAATATTCAAGAATTAATTCTT
CATCAGTATCAATCGGGTCTTGTAGTGACTAATCGTTCAGGTGCAATACTTAAAAACGCA
ATTTTTAGGGAAAAATGGGAACTATCAAATGATGATGTGCTTTTGGTTGAGAAAATCGGC
AGAGGAAATTTTGGTGATGTTTATAAAGCAAAGCTTAAAAATACGAAACAGGAAGTTGCG
GTTAAAACTTGTAAAATGACATTACCTGAAGAACAAAAAAAGAAGTTTTTGCAAGAAGGA
AGAATATTAAAGCAATATGATCATCCAAATATTGTAAAATTGATAGGCATTTGTGTACAA
AAACAACCAATTATGATTGTTATGGAATTGGTAGAAGGAGGAAGTCTTTTGATGTTTCTT
CGGAAAAATGCACAAATATTAGAATTAAAACAGATGCTACGAATGTGCAGTGACATTTCT
GCTGGCATGCAATATTTAGAATCAAAAAATTGCATTCATCGAGATTTAGCTGCTAGAAAT
TGTCTCATTGGTTCTGAAAATATTGTAAAAATTTCTGACTTTGGCATGTCAAGAGAAGAA
GAAGAGTATATTGTCTCTGATGGTATGAAGCAGATACCTATCAAGTGGACAGCACCAGAA
GCTTTAAATTGGGGCAAATATAATTCACTCACCGATGTATGGAGCTATGGAATTTTAATG
TTTGAAATATTCTCAAAAGGTGCAACTCCTTATTCAGGGATGTCGAATTCTAAAGCAAGA
GAGAAGATTGAAGAAGGATATAGACTGCCAGCACCAGAAGGTACACCAATCAAAGTTTAT
GAGCTTATGTTAAAATGTTGGAGTATAGAGCCTATAGATAGACCTCATTTTAATGAAATT
CATAATGAAATTACACATCTATTAAATCAGTAA

>g3711.t2 Gene=g3711 Length=790
MGLSTQGKNIHDVITARHESEIRLIEVMRKCLLLKVKCDRDYASSIQSVSVVGLKIDRID
DLNGSQIFKTWKRFMEELENQSKLIRKKMECLENICIDRISNILVEKRKIKKQCQDDHEK
IASRLFQFTDEVAKKKTEYNKQLEYYKQMRLRFEEHYIKSGRAGRKLDDVREKYQKACRK
LHLIHNEYVLLLHEATEVEKDYRTDLFPTFLSNQEALHEQFNENWNSILVDIAKLLDLSS
ADEFLKTQEQLSNGLKGSISKDEYNDILEKYKASPIVFHFDENLINDNVGKLLPNQLAVD
NLTIDWLKQKMLELEQSMKECQEEQQKLKQSNSSEQLTLNNLLNKSLVNIEGQNHSSQIV
DLKLKSLKNEERQMFKVLEIIKSSLNEVSLNELPSGCDDDLPSVVVENDEKYRNSTLTVS
PTQPLYLEPWFHGVLPREEVVRLLRNEGDFLVRETTRNDETQIVLSVCWNGHKHFIVQTT
ADNHYRFEGPSFANIQELILHQYQSGLVVTNRSGAILKNAIFREKWELSNDDVLLVEKIG
RGNFGDVYKAKLKNTKQEVAVKTCKMTLPEEQKKKFLQEGRILKQYDHPNIVKLIGICVQ
KQPIMIVMELVEGGSLLMFLRKNAQILELKQMLRMCSDISAGMQYLESKNCIHRDLAARN
CLIGSENIVKISDFGMSREEEEYIVSDGMKQIPIKWTAPEALNWGKYNSLTDVWSYGILM
FEIFSKGATPYSGMSNSKAREKIEEGYRLPAPEGTPIKVYELMLKCWSIEPIDRPHFNEI
HNEITHLLNQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
21 g3711.t2 CDD cd07657 F-BAR_Fes_Fer 6 238 2.16274E-84
20 g3711.t2 CDD cd10361 SH2_Fps_family 423 509 9.46134E-27
17 g3711.t2 Coils Coil Coil 75 95 -
16 g3711.t2 Coils Coil Coil 304 334 -
15 g3711.t2 Gene3D G3DSA:1.20.1270.60 Arfaptin 2 273 4.7E-36
14 g3711.t2 Gene3D G3DSA:3.30.505.10 SHC Adaptor Protein 415 527 6.6E-26
13 g3711.t2 Gene3D G3DSA:1.10.510.10 Transferase(Phosphotransferase) domain 1 528 790 3.8E-86
3 g3711.t2 PANTHER PTHR24418:SF418 TYROSINE-PROTEIN KINASE FER 64 785 2.7E-249
4 g3711.t2 PANTHER PTHR24418 TYROSINE-PROTEIN KINASE 64 785 2.7E-249
18 g3711.t2 PIRSF PIRSF000632 TyrPK_fps 1 420 6.6E-41
19 g3711.t2 PIRSF PIRSF000632 TyrPK_fps 412 790 7.3E-171
9 g3711.t2 PRINTS PR00109 Tyrosine kinase catalytic domain signature 608 621 1.4E-31
7 g3711.t2 PRINTS PR00109 Tyrosine kinase catalytic domain signature 645 663 1.4E-31
5 g3711.t2 PRINTS PR00109 Tyrosine kinase catalytic domain signature 692 702 1.4E-31
8 g3711.t2 PRINTS PR00109 Tyrosine kinase catalytic domain signature 711 733 1.4E-31
6 g3711.t2 PRINTS PR00109 Tyrosine kinase catalytic domain signature 755 777 1.4E-31
1 g3711.t2 Pfam PF00017 SH2 domain 430 501 1.5E-14
2 g3711.t2 Pfam PF07714 Protein tyrosine and serine/threonine kinase 535 783 2.1E-96
26 g3711.t2 ProSitePatterns PS00107 Protein kinases ATP-binding region signature. 539 562 -
25 g3711.t2 ProSitePatterns PS00109 Tyrosine protein kinases specific active-site signature. 651 663 -
27 g3711.t2 ProSiteProfiles PS51741 F-BAR domain profile. 1 263 20.359
28 g3711.t2 ProSiteProfiles PS50001 Src homology 2 (SH2) domain profile. 430 521 13.697
29 g3711.t2 ProSiteProfiles PS50011 Protein kinase domain profile. 533 784 40.047
23 g3711.t2 SMART SM00055 fch_2 1 92 0.0083
24 g3711.t2 SMART SM00252 SH2_5 428 508 4.3E-23
22 g3711.t2 SMART SM00219 tyrkin_6 533 784 4.2E-133
10 g3711.t2 SUPERFAMILY SSF103657 BAR/IMD domain-like 11 236 1.01E-20
12 g3711.t2 SUPERFAMILY SSF55550 SH2 domain 418 550 4.04E-24
11 g3711.t2 SUPERFAMILY SSF56112 Protein kinase-like (PK-like) 522 785 1.64E-80

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
GO:0018108 peptidyl-tyrosine 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