General information for g7977.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as ATP-dependent Clp protease ATP-binding subunit clpX-like, mitochondrial.
Parent gene
- The parent gene g7977 is located on chr_2: 27439373..27441555 (+ 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_2 | g7977 | g7977.t12 | isoform | g7977.t12 | 27436962 | 27439034 |
| chr_2 | g7977 | g7977.t12 | exon | g7977.t12.exon1 | 27436962 | 27437025 |
| chr_2 | g7977 | g7977.t12 | cds | g7977.t12.CDS1 | 27436962 | 27437025 |
| chr_2 | g7977 | g7977.t12 | exon | g7977.t12.exon2 | 27437719 | 27438498 |
| chr_2 | g7977 | g7977.t12 | cds | g7977.t12.CDS2 | 27437719 | 27438498 |
| chr_2 | g7977 | g7977.t12 | exon | g7977.t12.exon3 | 27438560 | 27438710 |
| chr_2 | g7977 | g7977.t12 | cds | g7977.t12.CDS3 | 27438560 | 27438710 |
| chr_2 | g7977 | g7977.t12 | exon | g7977.t12.exon4 | 27438766 | 27439034 |
| chr_2 | g7977 | g7977.t12 | cds | g7977.t12.CDS4 | 27438766 | 27439033 |
| chr_2 | g7977 | g7977.t12 | TSS | g7977.t12 | NA | NA |
| chr_2 | g7977 | g7977.t12 | TTS | g7977.t12 | NA | NA |
Sequences
>g7977.t12 Gene=g7977 Length=1264
ATGAGAGGCATACGAAACTCAATTAGTCTTCACAAATTTGCAACTTCTCCAAAAAATCGA
ACAGCGTATTTGTGTTTAGTGGCATCACAACAGCTTCACAATAATAATAATCAGATGTGC
TTAGCATCAGGCACTAATAACAGCAATAGTCCCGCTACAAACCTTTCACATGTTCGATAC
TTTCATTTAACACATATCTGTGATAAGTCGAATAAGGACCCAACAAATGGAAATGATAAA
AACAATAATAATTCGACAACATCAAGTGGTTCTAATAATAACAACAATAATAAAGACAAT
GGCAAAGACCCGAATAAAAAGAACACTCTTTCATGCCCAAAATGTGGCGATCCATGCACT
CATGTTGAAACTTTTGTAAATGCAACACGATTCGTCAAGTGTGAAAAATGTCATCATTTT
TTTGTGGTGCTTAGTGAGATGGACTCAAAAAAGACAGTCAAAGAAGAGTCTATTAAGGGA
ACAAAAAAACCACCGCCACCACCAAAAAAGATTATGGAATATTTGGACCGTCATGTAGTC
GGTCAAGAACTCGCCAAGAAGGTGCTATCAGTTGCAGTTTATAATCATTATAAACGCATT
TACCATAATTTGCCGCCACCATCAAATAACAATTCTACACAGTCAATTGATTCAATGGGA
AGAGGCAGTGATTTGTTGCATATTTCTGGCATAGGGCATACAATGCTTAGTTCAGCACCT
ACTGAAGTGCCACGTCCACCTTTATCGCCACCACAGCAACATCATCCTGGATCTGAATTA
TTAGAAGAAAAAAACCATACATTGAAATTAGAGAAAAGTAACATTTTAATGCTCGGACCA
ACAGGATCGGGAAAAACTTTATTAGCACAAACTATAGCGAAATGTTTGGATGTTCCATTT
GCCATTTGTGACTGTACTACATTAACTCAAGCTGGATATGTCGGAGAGGATATAGAAAGT
GTTATTGCTAAATTACTTCAAGATGCTAATTATAGTGTTGAAAGAGCTCAAACTGGAATA
GTTTTCCTTGATGAAGTCGATAAAATCGGCGCTGTTCCAGGAATCCATCAACTTCGCGAT
GTAGGTGGTGAAGGTGTTCAGCAAGGCATGCTCAAAATGCTCGAAGGAACAATCGTTAAT
GTTCCGGAAAGAAATTCACCGCGTAAACTTCGCGGCGAATCTGTACAGGTTGATACTACA
AACATTTTGTTTGTTGCTTCTGGTGCTTACACAGGATTAGATCGTTTAATTGCAAGGCGT
TTAA
>g7977.t12 Gene=g7977 Length=421
MRGIRNSISLHKFATSPKNRTAYLCLVASQQLHNNNNQMCLASGTNNSNSPATNLSHVRY
FHLTHICDKSNKDPTNGNDKNNNNSTTSSGSNNNNNNKDNGKDPNKKNTLSCPKCGDPCT
HVETFVNATRFVKCEKCHHFFVVLSEMDSKKTVKEESIKGTKKPPPPPKKIMEYLDRHVV
GQELAKKVLSVAVYNHYKRIYHNLPPPSNNNSTQSIDSMGRGSDLLHISGIGHTMLSSAP
TEVPRPPLSPPQQHHPGSELLEEKNHTLKLEKSNILMLGPTGSGKTLLAQTIAKCLDVPF
AICDCTTLTQAGYVGEDIESVIAKLLQDANYSVERAQTGIVFLDEVDKIGAVPGIHQLRD
VGGEGVQQGMLKMLEGTIVNVPERNSPRKLRGESVQVDTTNILFVASGAYTGLDRLIARR
L
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g7977.t12 | CDD | cd00009 | AAA | 272 | 421 | 1.10897E-16 |
| 5 | g7977.t12 | Coils | Coil | Coil | 418 | 421 | - |
| 8 | g7977.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 71 | 104 | - |
| 9 | g7977.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 76 | 99 | - |
| 2 | g7977.t12 | PANTHER | PTHR48102:SF7 | ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX-LIKE, MITOCHONDRIAL | 93 | 420 | 3.9E-121 |
| 3 | g7977.t12 | PANTHER | PTHR48102 | ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX-LIKE, MITOCHONDRIAL-RELATED | 93 | 420 | 3.9E-121 |
| 1 | g7977.t12 | Pfam | PF07724 | AAA domain (Cdc48 subfamily) | 271 | 414 | 5.7E-32 |
| 10 | g7977.t12 | ProSiteProfiles | PS51902 | ClpX zinc binding (ZB) domain profile. | 100 | 153 | 14.75 |
| 7 | g7977.t12 | SMART | SM00382 | AAA_5 | 271 | 421 | 3.5E-8 |
| 4 | g7977.t12 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 166 | 418 | 6.58E-37 |
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:0005524 | ATP binding | MF |
| GO:0008270 | zinc ion binding | MF |
| GO:0046983 | protein dimerization activity | MF |
| GO:0016887 | ATP hydrolysis 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.
