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.t4 TTS g6820.t4 18944895 18944895
chr_2 g6820 g6820.t4 isoform g6820.t4 18945725 18946610
chr_2 g6820 g6820.t4 exon g6820.t4.exon1 18945725 18946411
chr_2 g6820 g6820.t4 cds g6820.t4.CDS1 18945727 18946411
chr_2 g6820 g6820.t4 exon g6820.t4.exon2 18946522 18946610
chr_2 g6820 g6820.t4 cds g6820.t4.CDS2 18946522 18946610
chr_2 g6820 g6820.t4 TSS g6820.t4 18946838 18946838

Sequences

>g6820.t4 Gene=g6820 Length=776
ATGGAGGATATCTTCTATTGGTGTCGTGAAAATAACACAATTCAAGTTAGACTTTGGCTT
GATGATACAGAAAATGATTTTAACAAAGGTGATGATCATGGATTTTCAGCATTGCATTGG
TCAGCAAAGGAAGGACATACAAAATTAGTTGAGATGTTGCTTGCACGAGGAGCACGAGTT
AATGCCACTAATATGGGCGAAGATATTCCGCTTCATTTGGCAGCTGCCCACGGTCATATC
GATGTTGTGTTAATGTTGATTAAAGCAAAATCAGATATTAATGCACAAAATGAACATGGA
AACACGCCTCTTCATTATGCTTGCTTTTGGGGATATCAGCATATTGCTGAAGAGTTAGTA
AATCATGGTGCTCTGGTTTCACTTGCCAATAAAGATGGCGATACACCATTGGATAAAGCA
AAATCATTGTTGGCAAAACGTCTTCATGATTTGGCAATTGAAAGTGGTCAAGAATTGAAA
AAAATCAGCATCAAAGATAATCAATGGTTGGGACTAAAAACTCGTTCACGTGATGCAACA
CTTTCTCGCTATAAGGGTATCAACATTGAGGATTTGAAACTTCATACAAAAGTCTCAATC
AGTCCATCGGGTGAAACATGGCGTGGACGATGGCAAAATAATGATGTCATTGCAAAAATT
CTGACCATTCGTGAAATCACGCCTCGAGTGTCACGAGATTTCAACGAAGAATTCCCAAAA
TTGAGAATATTCTCTCATCCTAATATCCTTCCGCTCATTGGTGCTTGTAATTCACA

>g6820.t4 Gene=g6820 Length=258
MEDIFYWCRENNTIQVRLWLDDTENDFNKGDDHGFSALHWSAKEGHTKLVEMLLARGARV
NATNMGEDIPLHLAAAHGHIDVVLMLIKAKSDINAQNEHGNTPLHYACFWGYQHIAEELV
NHGALVSLANKDGDTPLDKAKSLLAKRLHDLAIESGQELKKISIKDNQWLGLKTRSRDAT
LSRYKGINIEDLKLHTKVSISPSGETWRGRWQNNDVIAKILTIREITPRVSRDFNEEFPK
LRIFSHPNILPLIGACNS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g6820.t4 Gene3D G3DSA:1.25.40.20 - 1 174 0.0000000
11 g6820.t4 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 181 258 0.0000000
4 g6820.t4 PANTHER PTHR24180 CYCLIN-DEPENDENT KINASE INHIBITOR 2C-RELATED 10 140 0.0000000
3 g6820.t4 PANTHER PTHR24180 CYCLIN-DEPENDENT KINASE INHIBITOR 2C-RELATED 70 150 0.0000000
16 g6820.t4 PIRSF PIRSF000654 ILK 1 258 0.0000000
2 g6820.t4 Pfam PF12796 Ankyrin repeats (3 copies) 5 64 0.0000016
1 g6820.t4 Pfam PF13637 Ankyrin repeats (many copies) 70 117 0.0000000
12 g6820.t4 ProSiteProfiles PS50297 Ankyrin repeat region circular profile. 26 140 37.5070000
15 g6820.t4 ProSiteProfiles PS50088 Ankyrin repeat profile. 33 65 13.3840000
13 g6820.t4 ProSiteProfiles PS50088 Ankyrin repeat profile. 66 98 11.9420000
14 g6820.t4 ProSiteProfiles PS50088 Ankyrin repeat profile. 99 131 11.8880000
7 g6820.t4 SMART SM00248 ANK_2a 33 62 0.0000320
8 g6820.t4 SMART SM00248 ANK_2a 66 95 0.0000480
9 g6820.t4 SMART SM00248 ANK_2a 99 128 0.0000760
5 g6820.t4 SUPERFAMILY SSF48403 Ankyrin repeat 5 142 0.0000000
6 g6820.t4 SUPERFAMILY SSF56112 Protein kinase-like (PK-like) 189 256 0.0000037

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:0005515 protein binding MF

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