Gene loci information

Transcript annotation

  • This transcript has been annotated as Integrin-linked protein kinase homolog pat-4.

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_2 g6820 g6820.t3 isoform g6820.t3 18944371 18946411
chr_2 g6820 g6820.t3 exon g6820.t3.exon1 18944371 18945462
chr_2 g6820 g6820.t3 TTS g6820.t3 18944398 18944398
chr_2 g6820 g6820.t3 cds g6820.t3.CDS1 18945079 18945462
chr_2 g6820 g6820.t3 exon g6820.t3.exon2 18945532 18946411
chr_2 g6820 g6820.t3 cds g6820.t3.CDS2 18945532 18946347
chr_2 g6820 g6820.t3 TSS g6820.t3 18946838 18946838

Sequences

>g6820.t3 Gene=g6820 Length=1972
TGATGATCATGGATTTTCAGCATTGCATTGGTCAGCAAAGGAAGGACATACAAAATTAGT
TGAGATGTTGCTTGCACGAGGAGCACGAGTTAATGCCACTAATATGGGCGAAGATATTCC
GCTTCATTTGGCAGCTGCCCACGGTCATATCGATGTTGTGTTAATGTTGATTAAAGCAAA
ATCAGATATTAATGCACAAAATGAACATGGAAACACGCCTCTTCATTATGCTTGCTTTTG
GGGATATCAGCATATTGCTGAAGAGTTAGTAAATCATGGTGCTCTGGTTTCACTTGCCAA
TAAAGATGGCGATACACCATTGGATAAAGCAAAATCATTGTTGGCAAAACGTCTTCATGA
TTTGGCAATTGAAAGTGGTCAAGAATTGAAAAAAATCAGCATCAAAGATAATCAATGGTT
GGGACTAAAAACTCGTTCACGTGATGCAACACTTTCTCGCTATAAGGGTATCAACATTGA
GGATTTGAAACTTCATACAAAAGTCTCAATCAGTCCATCGGGTGAAACATGGCGTGGACG
ATGGCAAAATAATGATGTCATTGCAAAAATTCTGACCATTCGTGAAATCACGCCTCGAGT
GTCACGAGATTTCAACGAAGAATTCCCAAAATTGAGAATATTCTCTCATCCTAATATCCT
TCCGCTCATTGGTGCTTGTAATTCACAGAAGCACTTAGTCACGATTAGTCAGTACATGCC
TAGAGGTTCACTTTATGATTTATTGCATTCGGCAGCTGGCATTGTTGTGGACACTGCCCA
AGCTGTCAGATTTGCTCTTGACATTGCAAAAGGAATGGCCTACTTACACTCGTTAGAGCG
AATCATTCCTGAATTTTTCCTCAACAGCTTTCATGTCATGATCGATGAGGATTTGACAGC
ACGCATTAATATGGGTGACTGCAAGTTTTCGTTTCAAGAACGTGGACGAATTTATCAGCC
AGCTTGGATGTCGCCAGAAACTTTACAACGAAAACGTGCCGATCGAAATTGGGAGGCATG
CGATATGTGGAGTTTTTCGATTGTTGTATGGGAATTAATGACTCGTGAGATTCCATTTGT
CGATTTATCACCAATGGAGTGTGGAATGAGAATTGCGACCGAGGGTCTTCGAGTTCAAAT
TCCACCCGGTGCTTCGGCACACTTGTCAAAGTTGATTAAAATTTGCATGAATGAGGAGGC
AGGAAAACGTCCACGTTTTGATATGGTTATACCAATTTTGGAGAAAATGGGTGCAAAGTT
CTAGGAAACTTATTTAAATTAACTTGTGTTCATACAAAAAATCTCAACAATCAGCAATAG
AACTAAATCCACACAAAAAATGAATCGAAATAGTGCCAACTTAACTCACAATTTTACTTT
TAAAGTATTTTTGACAAAAAAAAGCTTTTAATGATAAAGTGTCCTCTATTAATGTGCCTA
AACATGAGAAAAAAATAACTTTTATTGTTGTTGTAGAAACTTAATTTTTATGCTGTTACC
AGACTTTTAACTAAGTCATTAATTTTGTATTTAGAAACTTTTTTTAATTGACTCATGTGT
GAACATTTTGACAATTTAAAATTAATAATCGACTTATTGTTTTCAAAAAAATGTCAATTA
TAAATTATTAAGAAAAATTGACATTTTTGAATAAAAATGATTCAATTTATATGCCATGTG
TCTTGACATGCCCATGAAGTGAGTCGGGGTTTTTTTTGTTTTAAGTGCACACATGAGTGA
TTTTAATAATAATAGAAAATATTTTATATATGCTGGTAACATACTAAAAATCAAATTAGC
TTTTTTCTAACATTTACTTAATAATTTTTAATTGATATTAATTATTTTTGAATTTTTAAC
TTTTTAATGATCCATAATTTAATCAATACCGTAAAAAGCTGAAAATTATTTTTATAAAGA
AAAAAATAAATTAACATTTAAAAAATTTGTAAACTTTTTTGACTCTCATAAA

>g6820.t3 Gene=g6820 Length=399
MLLARGARVNATNMGEDIPLHLAAAHGHIDVVLMLIKAKSDINAQNEHGNTPLHYACFWG
YQHIAEELVNHGALVSLANKDGDTPLDKAKSLLAKRLHDLAIESGQELKKISIKDNQWLG
LKTRSRDATLSRYKGINIEDLKLHTKVSISPSGETWRGRWQNNDVIAKILTIREITPRVS
RDFNEEFPKLRIFSHPNILPLIGACNSQKHLVTISQYMPRGSLYDLLHSAAGIVVDTAQA
VRFALDIAKGMAYLHSLERIIPEFFLNSFHVMIDEDLTARINMGDCKFSFQERGRIYQPA
WMSPETLQRKRADRNWEACDMWSFSIVVWELMTREIPFVDLSPMECGMRIATEGLRVQIP
PGASAHLSKLIKICMNEEAGKRPRFDMVIPILEKMGAKF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g6820.t3 Gene3D G3DSA:1.25.40.20 - 1 123 0.000000
12 g6820.t3 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 130 217 0.000000
13 g6820.t3 Gene3D G3DSA:1.10.510.10 Transferase(Phosphotransferase) domain 1 218 397 0.000000
4 g6820.t3 PANTHER PTHR23257 SERINE-THREONINE PROTEIN KINASE 1 90 0.000000
6 g6820.t3 PANTHER PTHR23257:SF822 INTEGRIN-LINKED KINASE 1 90 0.000000
3 g6820.t3 PANTHER PTHR23257 SERINE-THREONINE PROTEIN KINASE 111 389 0.000000
5 g6820.t3 PANTHER PTHR23257:SF822 INTEGRIN-LINKED KINASE 111 389 0.000000
18 g6820.t3 PIRSF PIRSF000654 ILK 1 399 0.000000
1 g6820.t3 Pfam PF12796 Ankyrin repeats (3 copies) 2 75 0.000000
2 g6820.t3 Pfam PF07714 Protein tyrosine and serine/threonine kinase 152 390 0.000000
14 g6820.t3 ProSiteProfiles PS50297 Ankyrin repeat region circular profile. 1 89 30.502000
16 g6820.t3 ProSiteProfiles PS50088 Ankyrin repeat profile. 15 47 11.942000
15 g6820.t3 ProSiteProfiles PS50088 Ankyrin repeat profile. 48 80 11.888000
17 g6820.t3 ProSiteProfiles PS50011 Protein kinase domain profile. 141 392 21.573000
9 g6820.t3 SMART SM00248 ANK_2a 15 44 0.000048
10 g6820.t3 SMART SM00248 ANK_2a 48 77 0.000076
7 g6820.t3 SUPERFAMILY SSF48403 Ankyrin repeat 1 91 0.000000
8 g6820.t3 SUPERFAMILY SSF56112 Protein kinase-like (PK-like) 128 390 0.000000

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

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