Gene loci information

Transcript annotation

  • This transcript has been annotated as ATP-dependent Clp protease proteolytic subunit, mitochondrial.

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_1 g12988 g12988.t2 TSS g12988.t2 27379883 27379883
chr_1 g12988 g12988.t2 isoform g12988.t2 27379977 27380883
chr_1 g12988 g12988.t2 exon g12988.t2.exon1 27379977 27380019
chr_1 g12988 g12988.t2 exon g12988.t2.exon2 27380087 27380330
chr_1 g12988 g12988.t2 cds g12988.t2.CDS1 27380225 27380330
chr_1 g12988 g12988.t2 exon g12988.t2.exon3 27380391 27380507
chr_1 g12988 g12988.t2 cds g12988.t2.CDS2 27380391 27380507
chr_1 g12988 g12988.t2 exon g12988.t2.exon4 27380579 27380883
chr_1 g12988 g12988.t2 cds g12988.t2.CDS3 27380579 27380883
chr_1 g12988 g12988.t2 TTS g12988.t2 27380945 27380945

Sequences

>g12988.t2 Gene=g12988 Length=709
ATGAATTTCATTAAATCGGTGGCAATAAATAGTACTAAAGTAAAAAATTATAAATTCTAC
TGCGATAGCACAACAGAGAAGAAATTTGGGATTAGTGCCGATTGTGATTGAAGCGACAGG
TCGCGGAGAAAGAAGTTATGATATATTCTCAAGGTTGCTTAAAGAGCGAATTATTTGTCT
AATGGGGCCTGTAAATGATACAGTTAGCTCATTAATTGTCGCTCAATTATTATTTTTACA
ATCTGAAAACTCAACAAAACCAATTCACATGTATATCAATTCTCCCGGTGGATCAGTGAC
ATCCGGACTTGCTATTTATGATACTATGCAATACGTAAAGCCACCTATCGCTACTTGGTG
TGTTGGTCAAGCTTGTTCTATGGGGTCTTTATTATTGGCAGCAGGTGAATCAGGAATGAG
ACACTCATTGCCAAATTCACGTATCATGATTCATCAACCAACTGGTGGAGCTCAAGGACA
AGCGACTGATATCGCTATACAAGCTGAAGAAATATTAAAATTAAAGAAGAGACTAACTCG
TATATATGAAAAACACACAAAACAAGATTATCAAGTGTTATTTGAAAAAATGGAACGTGA
TACATTCTTAACTCCCGAAGAAGCAAAAGAGATGGGAATAATTGATGAAGTACTCGAACA
ACCACCAACACTCTCTGATAATATTTCAAATGACAACAGTAGTAGTTAG

>g12988.t2 Gene=g12988 Length=175
MGPVNDTVSSLIVAQLLFLQSENSTKPIHMYINSPGGSVTSGLAIYDTMQYVKPPIATWC
VGQACSMGSLLLAAGESGMRHSLPNSRIMIHQPTGGAQGQATDIAIQAEEILKLKKRLTR
IYEKHTKQDYQVLFEKMERDTFLTPEEAKEMGIIDEVLEQPPTLSDNISNDNSSS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g12988.t2 CDD cd07017 S14_ClpP_2 1 157 6.21094E-102
12 g12988.t2 Gene3D G3DSA:3.90.226.10 - 1 162 1.8E-69
2 g12988.t2 PANTHER PTHR10381:SF11 ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT, MITOCHONDRIAL 1 163 3.9E-85
3 g12988.t2 PANTHER PTHR10381 ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1 163 3.9E-85
5 g12988.t2 PRINTS PR00127 Clp protease catalytic subunit P signature 6 21 2.4E-41
7 g12988.t2 PRINTS PR00127 Clp protease catalytic subunit P signature 27 47 2.4E-41
4 g12988.t2 PRINTS PR00127 Clp protease catalytic subunit P signature 58 75 2.4E-41
6 g12988.t2 PRINTS PR00127 Clp protease catalytic subunit P signature 79 98 2.4E-41
8 g12988.t2 PRINTS PR00127 Clp protease catalytic subunit P signature 136 155 2.4E-41
1 g12988.t2 Pfam PF00574 Clp protease 2 160 2.3E-73
11 g12988.t2 ProSitePatterns PS00381 Endopeptidase Clp serine active site. 58 69 -
10 g12988.t2 ProSitePatterns PS00382 Endopeptidase Clp histidine active site. 80 93 -
9 g12988.t2 SUPERFAMILY SSF52096 ClpP/crotonase 2 161 3.59E-62

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:0004252 serine-type endopeptidase activity MF
GO:0006508 proteolysis BP
GO:0004176 ATP-dependent peptidase activity MF

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