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.t1 TTS g6820.t1 18944398 18944398
chr_2 g6820 g6820.t1 isoform g6820.t1 18945079 18946610
chr_2 g6820 g6820.t1 exon g6820.t1.exon1 18945079 18945462
chr_2 g6820 g6820.t1 cds g6820.t1.CDS1 18945079 18945462
chr_2 g6820 g6820.t1 exon g6820.t1.exon2 18945532 18946411
chr_2 g6820 g6820.t1 cds g6820.t1.CDS2 18945532 18946411
chr_2 g6820 g6820.t1 exon g6820.t1.exon3 18946522 18946610
chr_2 g6820 g6820.t1 cds g6820.t1.CDS3 18946522 18946610
chr_2 g6820 g6820.t1 TSS g6820.t1 18946838 18946838

Sequences

>g6820.t1 Gene=g6820 Length=1353
ATGGAGGATATCTTCTATTGGTGTCGTGAAAATAACACAATTCAAGTTAGACTTTGGCTT
GATGATACAGAAAATGATTTTAACAAAGGTGATGATCATGGATTTTCAGCATTGCATTGG
TCAGCAAAGGAAGGACATACAAAATTAGTTGAGATGTTGCTTGCACGAGGAGCACGAGTT
AATGCCACTAATATGGGCGAAGATATTCCGCTTCATTTGGCAGCTGCCCACGGTCATATC
GATGTTGTGTTAATGTTGATTAAAGCAAAATCAGATATTAATGCACAAAATGAACATGGA
AACACGCCTCTTCATTATGCTTGCTTTTGGGGATATCAGCATATTGCTGAAGAGTTAGTA
AATCATGGTGCTCTGGTTTCACTTGCCAATAAAGATGGCGATACACCATTGGATAAAGCA
AAATCATTGTTGGCAAAACGTCTTCATGATTTGGCAATTGAAAGTGGTCAAGAATTGAAA
AAAATCAGCATCAAAGATAATCAATGGTTGGGACTAAAAACTCGTTCACGTGATGCAACA
CTTTCTCGCTATAAGGGTATCAACATTGAGGATTTGAAACTTCATACAAAAGTCTCAATC
AGTCCATCGGGTGAAACATGGCGTGGACGATGGCAAAATAATGATGTCATTGCAAAAATT
CTGACCATTCGTGAAATCACGCCTCGAGTGTCACGAGATTTCAACGAAGAATTCCCAAAA
TTGAGAATATTCTCTCATCCTAATATCCTTCCGCTCATTGGTGCTTGTAATTCACAGAAG
CACTTAGTCACGATTAGTCAGTACATGCCTAGAGGTTCACTTTATGATTTATTGCATTCG
GCAGCTGGCATTGTTGTGGACACTGCCCAAGCTGTCAGATTTGCTCTTGACATTGCAAAA
GGAATGGCCTACTTACACTCGTTAGAGCGAATCATTCCTGAATTTTTCCTCAACAGCTTT
CATGTCATGATCGATGAGGATTTGACAGCACGCATTAATATGGGTGACTGCAAGTTTTCG
TTTCAAGAACGTGGACGAATTTATCAGCCAGCTTGGATGTCGCCAGAAACTTTACAACGA
AAACGTGCCGATCGAAATTGGGAGGCATGCGATATGTGGAGTTTTTCGATTGTTGTATGG
GAATTAATGACTCGTGAGATTCCATTTGTCGATTTATCACCAATGGAGTGTGGAATGAGA
ATTGCGACCGAGGGTCTTCGAGTTCAAATTCCACCCGGTGCTTCGGCACACTTGTCAAAG
TTGATTAAAATTTGCATGAATGAGGAGGCAGGAAAACGTCCACGTTTTGATATGGTTATA
CCAATTTTGGAGAAAATGGGTGCAAAGTTCTAG

>g6820.t1 Gene=g6820 Length=450
MEDIFYWCRENNTIQVRLWLDDTENDFNKGDDHGFSALHWSAKEGHTKLVEMLLARGARV
NATNMGEDIPLHLAAAHGHIDVVLMLIKAKSDINAQNEHGNTPLHYACFWGYQHIAEELV
NHGALVSLANKDGDTPLDKAKSLLAKRLHDLAIESGQELKKISIKDNQWLGLKTRSRDAT
LSRYKGINIEDLKLHTKVSISPSGETWRGRWQNNDVIAKILTIREITPRVSRDFNEEFPK
LRIFSHPNILPLIGACNSQKHLVTISQYMPRGSLYDLLHSAAGIVVDTAQAVRFALDIAK
GMAYLHSLERIIPEFFLNSFHVMIDEDLTARINMGDCKFSFQERGRIYQPAWMSPETLQR
KRADRNWEACDMWSFSIVVWELMTREIPFVDLSPMECGMRIATEGLRVQIPPGASAHLSK
LIKICMNEEAGKRPRFDMVIPILEKMGAKF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g6820.t1 Gene3D G3DSA:1.25.40.20 - 1 174 0.000000
14 g6820.t1 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 181 268 0.000000
15 g6820.t1 Gene3D G3DSA:1.10.510.10 Transferase(Phosphotransferase) domain 1 269 448 0.000000
4 g6820.t1 PANTHER PTHR23257 SERINE-THREONINE PROTEIN KINASE 50 141 0.000000
6 g6820.t1 PANTHER PTHR23257:SF822 INTEGRIN-LINKED KINASE 50 141 0.000000
5 g6820.t1 PANTHER PTHR23257 SERINE-THREONINE PROTEIN KINASE 162 440 0.000000
7 g6820.t1 PANTHER PTHR23257:SF822 INTEGRIN-LINKED KINASE 162 440 0.000000
21 g6820.t1 PIRSF PIRSF000654 ILK 1 450 0.000000
2 g6820.t1 Pfam PF12796 Ankyrin repeats (3 copies) 5 64 0.000004
1 g6820.t1 Pfam PF13637 Ankyrin repeats (many copies) 70 117 0.000000
3 g6820.t1 Pfam PF07714 Protein tyrosine and serine/threonine kinase 203 441 0.000000
16 g6820.t1 ProSiteProfiles PS50297 Ankyrin repeat region circular profile. 26 140 37.507000
19 g6820.t1 ProSiteProfiles PS50088 Ankyrin repeat profile. 33 65 13.384000
17 g6820.t1 ProSiteProfiles PS50088 Ankyrin repeat profile. 66 98 11.942000
18 g6820.t1 ProSiteProfiles PS50088 Ankyrin repeat profile. 99 131 11.888000
20 g6820.t1 ProSiteProfiles PS50011 Protein kinase domain profile. 192 443 21.573000
10 g6820.t1 SMART SM00248 ANK_2a 33 62 0.000032
11 g6820.t1 SMART SM00248 ANK_2a 66 95 0.000048
12 g6820.t1 SMART SM00248 ANK_2a 99 128 0.000076
8 g6820.t1 SUPERFAMILY SSF48403 Ankyrin repeat 5 142 0.000000
9 g6820.t1 SUPERFAMILY SSF56112 Protein kinase-like (PK-like) 179 441 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

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