Gene loci information

Transcript annotation

  • This transcript has been annotated as Atypical protein kinase C.

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 g5649 g5649.t2 isoform g5649.t2 10884901 10885894
chr_2 g5649 g5649.t2 exon g5649.t2.exon1 10884901 10884903
chr_2 g5649 g5649.t2 exon g5649.t2.exon2 10885002 10885894
chr_2 g5649 g5649.t2 cds g5649.t2.CDS1 10885120 10885893
chr_2 g5649 g5649.t2 TSS g5649.t2 NA NA
chr_2 g5649 g5649.t2 TTS g5649.t2 NA NA

Sequences

>g5649.t2 Gene=g5649 Length=896
AAGTTTTATCTACAATTATCAATTTACTTTTCTAAATAAATGTGTGACATTTTCATTCAC
AACTGACTCACAATTGTGGAAAATAACTAAGAAAAACAAAAAATTTAAAAATTTAGATTG
AATGAATAGAGGAGCATATAGCAATAGCAAAATGCCCGTAGTCAACAGTAACAACAACGA
CTCGTCGGCGCTTGCAAATGACGTTAAAGTGAAAATTGCCTATAATGGTGAAGTGCTTAT
CTTTTATATTGATGAAAACATCACGTATGAAGAATTGTGTAAAGAAATTCGCGGCATTTG
TCGTTTTGCACCGGATCAAGTCTTTACAATGAAATGGATTGATGAAGAAAATGATCCATG
CACAATCAGCTGTCAAATGGAATTAAATGAAGCAATTCGCTTATATGAAGTAAATCGCGA
TTCTGAACTTTTTATTCATGTCTTTCCAAATGCACCCGCCGCACCTGGATTATCATGCAT
TGGTGAAGATAAGAGTATATATAGACGTGGTGCAAGACGTTGGCGAAAACTTTATCGCAT
CAATGGACATATTTTTCAAGCAAAGAGATTTAATCGACGAGCATTTTGCGCATTTTGTCA
CGATCGTATTTGGGGTTTAGGTAGACAAGGTTTCAAATGCATTCAATGCAAACTGTTAGT
ACACAAAAAGTGTCACAAAATGCTACAAAAGCCCTGTAATGAGCAAGTTGAGCCAATTGA
TAGAATTGAACGTAATGGCGAAAGTGATCAAAAAACTGCACATCCAGAAGTGTCAACAAC
AATTGTCGAATTTCAATCAGGTGAAGGCGATCAAGTTGCTGTCGAATCACCACCACAGTC
GCACACTGATGAACCACTTGAGCCGGGCTCACAGCGGCAATATTCTCTTATTGATT

>g5649.t2 Gene=g5649 Length=258
MNRGAYSNSKMPVVNSNNNDSSALANDVKVKIAYNGEVLIFYIDENITYEELCKEIRGIC
RFAPDQVFTMKWIDEENDPCTISCQMELNEAIRLYEVNRDSELFIHVFPNAPAAPGLSCI
GEDKSIYRRGARRWRKLYRINGHIFQAKRFNRRAFCAFCHDRIWGLGRQGFKCIQCKLLV
HKKCHKMLQKPCNEQVEPIDRIERNGESDQKTAHPEVSTTIVEFQSGEGDQVAVESPPQS
HTDEPLEPGSQRQYSLID

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g5649.t2 CDD cd06404 PB1_aPKC 28 110 9.19974E-47
13 g5649.t2 CDD cd00029 C1 143 192 4.12037E-15
11 g5649.t2 Gene3D G3DSA:3.10.20.90 - 22 110 8.3E-40
12 g5649.t2 Gene3D G3DSA:3.30.60.20 - 127 195 4.0E-21
18 g5649.t2 MobiDBLite mobidb-lite consensus disorder prediction 228 258 -
3 g5649.t2 PANTHER PTHR24351:SF216 PROTEIN KINASE C 37 219 1.1E-86
4 g5649.t2 PANTHER PTHR24351 RIBOSOMAL PROTEIN S6 KINASE 37 219 1.1E-86
8 g5649.t2 PRINTS PR00008 Diacylglycerol/phorbol-ester binding signature 140 154 6.5E-8
5 g5649.t2 PRINTS PR00008 Diacylglycerol/phorbol-ester binding signature 156 165 6.5E-8
7 g5649.t2 PRINTS PR00008 Diacylglycerol/phorbol-ester binding signature 169 180 6.5E-8
6 g5649.t2 PRINTS PR00008 Diacylglycerol/phorbol-ester binding signature 181 193 6.5E-8
1 g5649.t2 Pfam PF00564 PB1 domain 28 109 7.9E-14
2 g5649.t2 Pfam PF00130 Phorbol esters/diacylglycerol binding domain (C1 domain) 143 193 2.1E-12
17 g5649.t2 ProSitePatterns PS00479 Zinc finger phorbol-ester/DAG-type signature. 143 192 -
19 g5649.t2 ProSiteProfiles PS51745 PB1 domain profile. 27 110 24.61
20 g5649.t2 ProSiteProfiles PS50081 Zinc finger phorbol-ester/DAG-type profile. 142 192 14.49
15 g5649.t2 SMART SM00666 PB1_new 27 108 1.8E-20
16 g5649.t2 SMART SM00109 c1_12 143 192 4.7E-12
10 g5649.t2 SUPERFAMILY SSF54277 CAD & PB1 domains 25 109 5.64E-27
9 g5649.t2 SUPERFAMILY SSF57889 Cysteine-rich domain 122 193 2.54E-19

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5649/g5649.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5649.t2.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005515 protein binding MF
GO:0035556 intracellular signal transduction 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