Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t4 TSS g12988.t4 27379883 27379883
chr_1 g12988 g12988.t4 isoform g12988.t4 27379977 27380883
chr_1 g12988 g12988.t4 exon g12988.t4.exon1 27379977 27380015
chr_1 g12988 g12988.t4 exon g12988.t4.exon2 27380087 27380507
chr_1 g12988 g12988.t4 cds g12988.t4.CDS1 27380429 27380507
chr_1 g12988 g12988.t4 exon g12988.t4.exon3 27380579 27380883
chr_1 g12988 g12988.t4 cds g12988.t4.CDS2 27380579 27380883
chr_1 g12988 g12988.t4 TTS g12988.t4 27380945 27380945

Sequences

>g12988.t4 Gene=g12988 Length=765
ATGAATTTCATTAAATCGGTGGCAATAAATAGTACTAAAAAAATTATAAATTCTACTGCG
ATAGCACAACAGAGAAGAAATTTGGGATTAGTGCCGATTGTGATTGAAGCGACAGGTCGC
GGAGAAAGAAGTTATGATATATTCTCAAGGTTGCTTAAAGAGCGAATTATTTGTCTAATG
GGGCCTGTAAATGATACAGTTAGCTCATTAATTGTCGCTCAATTATTATTTTTACAATCT
GAAAACTCAACAAAACCAATTCACATGTATATCAATTCTCCCGGTATAGATAGATATCTT
TTTAGTTTTTAAATGTTTTAAAATTGTTATAATCATTAAATAGGTGGATCAGTGACATCC
GGACTTGCTATTTATGATACTATGCAATACGTAAAGCCACCTATCGCTACTTGGTGTGTT
GGTCAAGCTTGTTCTATGGGGTCTTTATTATTGGCAGCAGGTGAATCAGGAATGAGACAC
TCATTGCCAAATTCACGTATCATGATTCATCAACCAACTGGTGGAGCTCAAGGACAAGCG
ACTGATATCGCTATACAAGCTGAAGAAATATTAAAATTAAAGAAGAGACTAACTCGTATA
TATGAAAAACACACAAAACAAGATTATCAAGTGTTATTTGAAAAAATGGAACGTGATACA
TTCTTAACTCCCGAAGAAGCAAAAGAGATGGGAATAATTGATGAAGTACTCGAACAACCA
CCAACACTCTCTGATAATATTTCAAATGACAACAGTAGTAGTTAG

>g12988.t4 Gene=g12988 Length=127
MQYVKPPIATWCVGQACSMGSLLLAAGESGMRHSLPNSRIMIHQPTGGAQGQATDIAIQA
EEILKLKKRLTRIYEKHTKQDYQVLFEKMERDTFLTPEEAKEMGIIDEVLEQPPTLSDNI
SNDNSSS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g12988.t4 CDD cd07017 S14_ClpP_2 1 109 2.90436E-65
8 g12988.t4 Gene3D G3DSA:3.90.226.10 - 1 115 7.1E-44
12 g12988.t4 MobiDBLite mobidb-lite consensus disorder prediction 108 127 -
2 g12988.t4 PANTHER PTHR10381:SF11 ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT, MITOCHONDRIAL 1 115 1.6E-53
3 g12988.t4 PANTHER PTHR10381 ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1 115 1.6E-53
5 g12988.t4 PRINTS PR00127 Clp protease catalytic subunit P signature 10 27 6.1E-25
6 g12988.t4 PRINTS PR00127 Clp protease catalytic subunit P signature 31 50 6.1E-25
4 g12988.t4 PRINTS PR00127 Clp protease catalytic subunit P signature 88 107 6.1E-25
1 g12988.t4 Pfam PF00574 Clp protease 1 112 3.9E-48
11 g12988.t4 ProSitePatterns PS00381 Endopeptidase Clp serine active site. 10 21 -
10 g12988.t4 ProSitePatterns PS00382 Endopeptidase Clp histidine active site. 32 45 -
13 g12988.t4 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile. 1 17 5.0
7 g12988.t4 SUPERFAMILY SSF52096 ClpP/crotonase 1 113 3.8E-40

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.

Raw TPM values