General information for g12988.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as ATP-dependent Clp protease proteolytic subunit, mitochondrial.
Parent gene
- The parent gene g12988 is located on chr_1: 27380087..27380883 (+ strand)
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.t1 | TSS | g12988.t1 | 27379883 | 27379883 |
| chr_1 | g12988 | g12988.t1 | isoform | g12988.t1 | 27379977 | 27380883 |
| chr_1 | g12988 | g12988.t1 | exon | g12988.t1.exon1 | 27379977 | 27380015 |
| chr_1 | g12988 | g12988.t1 | cds | g12988.t1.CDS1 | 27379977 | 27380015 |
| chr_1 | g12988 | g12988.t1 | exon | g12988.t1.exon2 | 27380087 | 27380330 |
| chr_1 | g12988 | g12988.t1 | cds | g12988.t1.CDS2 | 27380087 | 27380330 |
| chr_1 | g12988 | g12988.t1 | exon | g12988.t1.exon3 | 27380391 | 27380507 |
| chr_1 | g12988 | g12988.t1 | cds | g12988.t1.CDS3 | 27380391 | 27380507 |
| chr_1 | g12988 | g12988.t1 | exon | g12988.t1.exon4 | 27380579 | 27380883 |
| chr_1 | g12988 | g12988.t1 | cds | g12988.t1.CDS4 | 27380579 | 27380883 |
| chr_1 | g12988 | g12988.t1 | TTS | g12988.t1 | 27380945 | 27380945 |
Sequences
>g12988.t1 Gene=g12988 Length=705
ATGAATTTCATTAAATCGGTGGCAATAAATAGTACTAAAAAAATTATAAATTCTACTGCG
ATAGCACAACAGAGAAGAAATTTGGGATTAGTGCCGATTGTGATTGAAGCGACAGGTCGC
GGAGAAAGAAGTTATGATATATTCTCAAGGTTGCTTAAAGAGCGAATTATTTGTCTAATG
GGGCCTGTAAATGATACAGTTAGCTCATTAATTGTCGCTCAATTATTATTTTTACAATCT
GAAAACTCAACAAAACCAATTCACATGTATATCAATTCTCCCGGTGGATCAGTGACATCC
GGACTTGCTATTTATGATACTATGCAATACGTAAAGCCACCTATCGCTACTTGGTGTGTT
GGTCAAGCTTGTTCTATGGGGTCTTTATTATTGGCAGCAGGTGAATCAGGAATGAGACAC
TCATTGCCAAATTCACGTATCATGATTCATCAACCAACTGGTGGAGCTCAAGGACAAGCG
ACTGATATCGCTATACAAGCTGAAGAAATATTAAAATTAAAGAAGAGACTAACTCGTATA
TATGAAAAACACACAAAACAAGATTATCAAGTGTTATTTGAAAAAATGGAACGTGATACA
TTCTTAACTCCCGAAGAAGCAAAAGAGATGGGAATAATTGATGAAGTACTCGAACAACCA
CCAACACTCTCTGATAATATTTCAAATGACAACAGTAGTAGTTAG
>g12988.t1 Gene=g12988 Length=234
MNFIKSVAINSTKKIINSTAIAQQRRNLGLVPIVIEATGRGERSYDIFSRLLKERIICLM
GPVNDTVSSLIVAQLLFLQSENSTKPIHMYINSPGGSVTSGLAIYDTMQYVKPPIATWCV
GQACSMGSLLLAAGESGMRHSLPNSRIMIHQPTGGAQGQATDIAIQAEEILKLKKRLTRI
YEKHTKQDYQVLFEKMERDTFLTPEEAKEMGIIDEVLEQPPTLSDNISNDNSSS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g12988.t1 | CDD | cd07017 | S14_ClpP_2 | 46 | 216 | 2.11102E-110 |
| 11 | g12988.t1 | Gene3D | G3DSA:3.90.226.10 | - | 16 | 221 | 7.3E-83 |
| 4 | g12988.t1 | Hamap | MF_00444 | ATP-dependent Clp protease proteolytic subunit [clpP]. | 30 | 220 | 39.437588 |
| 2 | g12988.t1 | PANTHER | PTHR10381:SF11 | ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT, MITOCHONDRIAL | 16 | 222 | 4.8E-103 |
| 3 | g12988.t1 | PANTHER | PTHR10381 | ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT | 16 | 222 | 4.8E-103 |
| 7 | g12988.t1 | PRINTS | PR00127 | Clp protease catalytic subunit P signature | 46 | 61 | 3.9E-46 |
| 9 | g12988.t1 | PRINTS | PR00127 | Clp protease catalytic subunit P signature | 86 | 106 | 3.9E-46 |
| 6 | g12988.t1 | PRINTS | PR00127 | Clp protease catalytic subunit P signature | 117 | 134 | 3.9E-46 |
| 5 | g12988.t1 | PRINTS | PR00127 | Clp protease catalytic subunit P signature | 138 | 157 | 3.9E-46 |
| 8 | g12988.t1 | PRINTS | PR00127 | Clp protease catalytic subunit P signature | 195 | 214 | 3.9E-46 |
| 1 | g12988.t1 | Pfam | PF00574 | Clp protease | 40 | 219 | 4.8E-82 |
| 14 | g12988.t1 | ProSitePatterns | PS00381 | Endopeptidase Clp serine active site. | 117 | 128 | - |
| 13 | g12988.t1 | ProSitePatterns | PS00382 | Endopeptidase Clp histidine active site. | 139 | 152 | - |
| 10 | g12988.t1 | SUPERFAMILY | SSF52096 | ClpP/crotonase | 38 | 220 | 7.77E-70 |
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 transcript has been annotated with K01358 (ATP-dependent Clp protease, protease subunit)
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.
