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.t5 TTS g3711.t5 27578150 27578150
chr_3 g3711 g3711.t5 isoform g3711.t5 27578866 27584122
chr_3 g3711 g3711.t5 exon g3711.t5.exon1 27578866 27579400
chr_3 g3711 g3711.t5 cds g3711.t5.CDS1 27578867 27579400
chr_3 g3711 g3711.t5 exon g3711.t5.exon2 27579462 27579659
chr_3 g3711 g3711.t5 cds g3711.t5.CDS2 27579462 27579659
chr_3 g3711 g3711.t5 exon g3711.t5.exon3 27583486 27583878
chr_3 g3711 g3711.t5 cds g3711.t5.CDS3 27583486 27583488
chr_3 g3711 g3711.t5 exon g3711.t5.exon4 27583991 27584122
chr_3 g3711 g3711.t5 TSS g3711.t5 27584122 27584122

Sequences

>g3711.t5 Gene=g3711 Length=1258
AGTCTCATAAAAGAACGATCACTCTAAAGACGTGTATGTCTCGTTGTTTAAATATTTTTT
TTCATTTTATATTTTTAAATCATTAAAAGTGGAATTTTTGATTATTGCGAACTCTGCAAT
TTCTTATAAACTTCTCTCATAAGAAAATGAAAAGAAAATAATCAGAAAAAAGTAATGCAA
AAATTAATAAGAAAGAGAGAAAATTCTCTAGTGTGTGACAAATAATTAAAGACAAGACCA
ACCTACCTAGTTGCAATCGTTGATAAAATAAAAAAATCCACAAGCGAGAAAATAAGAAGA
AGTACACATTACTGTAAATTTAATTTATCGAAAAAATGGGACTCTCAACACAGGGAAAGA
ACATTCACGATGTAATAACTGCACGACATGAGTCCGAAATTCGTCTCATCGAAGTTATGC
GTAAATGTTTATTACTAAAAGTAAAGTGCGATCGTGATTATGCGTCTTCAATCCAGAGTG
TTTCCGTCGTTGGTCTCAAAATTGATCGAATAGACGATCTAAATGCTTACAGTTTCACCG
ACTCAGCCCTTATATCTTGAACCATGGTTTCATGGTGTGCTACCAAGAGAAGAAGTTGTA
CGATTATTACGAAATGAAGGTGATTTTTTGGTACGCGAAACAACTAGAAACGATGAAACT
CAAATTGTATTGAGTGTCTGTTGGAATGGACATAAACATTTTATTGTGCAAACGACTGCT
GATAACCATTATCGATTTGAAGGTCCATCATTTGCGAATATTCAAGAATTAATTCTTCAT
CAGTATCAATCGGGTCTTGTAGTGACTAATCGTTCAGGTGCAATACTTAAAAACGCAATT
TTTAGGGAAAAATGGGAACTATCAAATGATGATGTGCTTTTGGTTGAGAAAATCGGCAGA
GGAAATTTTGGTGATGTTTATAAAGCAAAGCTTAAAAATACGAAACAGGAAGTTGCGGTT
AAAACTTGTAAAATGACATTACCTGAAGAACAAAAAAAGAAGTTTTTGCAAGAAGGAAGA
ATATTAAAGCAATATGATCATCCAAATATTGTAAAATTGATAGGCATTTGTGTACAAAAA
CAACCAATTATGATTGTTATGGAATTGGTAGAAGGAGGAAGTCTTTTGATGTTTCTTCGG
AAAAATGCACAAATATTAGAATTAAAACAGATGCTACGAATGTGCAGTGACATTTCTGCT
GGCATGCAATATTTAGAATCAAAAAATTGCATTCATCGAGATTTAGCTGCTAGAAATT

>g3711.t5 Gene=g3711 Length=245
MLTVSPTQPLYLEPWFHGVLPREEVVRLLRNEGDFLVRETTRNDETQIVLSVCWNGHKHF
IVQTTADNHYRFEGPSFANIQELILHQYQSGLVVTNRSGAILKNAIFREKWELSNDDVLL
VEKIGRGNFGDVYKAKLKNTKQEVAVKTCKMTLPEEQKKKFLQEGRILKQYDHPNIVKLI
GICVQKQPIMIVMELVEGGSLLMFLRKNAQILELKQMLRMCSDISAGMQYLESKNCIHRD
LAARN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g3711.t5 CDD cd10361 SH2_Fps_family 8 94 3.1429E-29
12 g3711.t5 Gene3D G3DSA:3.30.505.10 SHC Adaptor Protein 3 111 8.8E-27
10 g3711.t5 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 112 197 2.6E-34
11 g3711.t5 Gene3D G3DSA:1.10.510.10 Transferase(Phosphotransferase) domain 1 198 245 1.1E-9
3 g3711.t5 PANTHER PTHR24418:SF418 TYROSINE-PROTEIN KINASE FER 10 245 1.5E-126
4 g3711.t5 PANTHER PTHR24418 TYROSINE-PROTEIN KINASE 10 245 1.5E-126
7 g3711.t5 PRINTS PR00401 SH2 domain signature 15 29 2.8E-5
5 g3711.t5 PRINTS PR00401 SH2 domain signature 32 42 2.8E-5
6 g3711.t5 PRINTS PR00401 SH2 domain signature 76 90 2.8E-5
1 g3711.t5 Pfam PF00017 SH2 domain 15 86 2.3E-15
2 g3711.t5 Pfam PF07714 Protein tyrosine and serine/threonine kinase 120 245 5.4E-45
14 g3711.t5 ProSitePatterns PS00107 Protein kinases ATP-binding region signature. 124 147 -
17 g3711.t5 ProSiteProfiles PS50001 Src homology 2 (SH2) domain profile. 15 106 13.697
18 g3711.t5 ProSiteProfiles PS50011 Protein kinase domain profile. 118 245 25.333
16 g3711.t5 SMART SM00252 SH2_5 13 93 4.3E-23
15 g3711.t5 SMART SM00219 tyrkin_6 118 245 3.7E-12
9 g3711.t5 SUPERFAMILY SSF55550 SH2 domain 5 135 9.42E-25
8 g3711.t5 SUPERFAMILY SSF56112 Protein kinase-like (PK-like) 94 245 1.36E-42

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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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