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.t5 TSS g12988.t5 27379883 27379883
chr_1 g12988 g12988.t5 isoform g12988.t5 27379977 27380883
chr_1 g12988 g12988.t5 exon g12988.t5.exon1 27379977 27380007
chr_1 g12988 g12988.t5 exon g12988.t5.exon2 27380087 27380330
chr_1 g12988 g12988.t5 cds g12988.t5.CDS1 27380225 27380330
chr_1 g12988 g12988.t5 exon g12988.t5.exon3 27380400 27380507
chr_1 g12988 g12988.t5 cds g12988.t5.CDS2 27380400 27380507
chr_1 g12988 g12988.t5 exon g12988.t5.exon4 27380579 27380883
chr_1 g12988 g12988.t5 cds g12988.t5.CDS3 27380579 27380883
chr_1 g12988 g12988.t5 TTS g12988.t5 27380945 27380945

Sequences

>g12988.t5 Gene=g12988 Length=688
ATGAATTTCATTAAATCGGTGGCAATAAATAAAAATTATAAATTCTACTGCGATAGCACA
ACAGAGAAGAAATTTGGGATTAGTGCCGATTGTGATTGAAGCGACAGGTCGCGGAGAAAG
AAGTTATGATATATTCTCAAGGTTGCTTAAAGAGCGAATTATTTGTCTAATGGGGCCTGT
AAATGATACAGTTAGCTCATTAATTGTCGCTCAATTATTATTTTTACAATCTGAAAACTC
AACAAAACCAATTCACATGTATATCAATTCTCCCGTGACATCCGGACTTGCTATTTATGA
TACTATGCAATACGTAAAGCCACCTATCGCTACTTGGTGTGTTGGTCAAGCTTGTTCTAT
GGGGTCTTTATTATTGGCAGCAGGTGAATCAGGAATGAGACACTCATTGCCAAATTCACG
TATCATGATTCATCAACCAACTGGTGGAGCTCAAGGACAAGCGACTGATATCGCTATACA
AGCTGAAGAAATATTAAAATTAAAGAAGAGACTAACTCGTATATATGAAAAACACACAAA
ACAAGATTATCAAGTGTTATTTGAAAAAATGGAACGTGATACATTCTTAACTCCCGAAGA
AGCAAAAGAGATGGGAATAATTGATGAAGTACTCGAACAACCACCAACACTCTCTGATAA
TATTTCAAATGACAACAGTAGTAGTTAG

>g12988.t5 Gene=g12988 Length=172
MGPVNDTVSSLIVAQLLFLQSENSTKPIHMYINSPVTSGLAIYDTMQYVKPPIATWCVGQ
ACSMGSLLLAAGESGMRHSLPNSRIMIHQPTGGAQGQATDIAIQAEEILKLKKRLTRIYE
KHTKQDYQVLFEKMERDTFLTPEEAKEMGIIDEVLEQPPTLSDNISNDNSSS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g12988.t5 CDD cd07017 S14_ClpP_2 1 154 6.78572E-97
12 g12988.t5 Gene3D G3DSA:3.90.226.10 - 1 159 9.5E-63
2 g12988.t5 PANTHER PTHR10381:SF11 ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT, MITOCHONDRIAL 1 160 1.8E-79
3 g12988.t5 PANTHER PTHR10381 ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1 160 1.8E-79
5 g12988.t5 PRINTS PR00127 Clp protease catalytic subunit P signature 6 21 1.2E-28
6 g12988.t5 PRINTS PR00127 Clp protease catalytic subunit P signature 24 44 1.2E-28
8 g12988.t5 PRINTS PR00127 Clp protease catalytic subunit P signature 55 72 1.2E-28
7 g12988.t5 PRINTS PR00127 Clp protease catalytic subunit P signature 76 95 1.2E-28
4 g12988.t5 PRINTS PR00127 Clp protease catalytic subunit P signature 133 152 1.2E-28
1 g12988.t5 Pfam PF00574 Clp protease 2 157 2.4E-67
11 g12988.t5 ProSitePatterns PS00381 Endopeptidase Clp serine active site. 55 66 -
10 g12988.t5 ProSitePatterns PS00382 Endopeptidase Clp histidine active site. 77 90 -
9 g12988.t5 SUPERFAMILY SSF52096 ClpP/crotonase 2 158 3.22E-56

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

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. There were no conditions that were differentially expressed