General information for g7977.t1
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.t1 | isoform | g7977.t1 | 27436962 | 27439850 |
| chr_2 | g7977 | g7977.t1 | exon | g7977.t1.exon1 | 27436962 | 27437025 |
| chr_2 | g7977 | g7977.t1 | cds | g7977.t1.CDS1 | 27436962 | 27437025 |
| chr_2 | g7977 | g7977.t1 | exon | g7977.t1.exon2 | 27437719 | 27438498 |
| chr_2 | g7977 | g7977.t1 | cds | g7977.t1.CDS2 | 27437719 | 27438498 |
| chr_2 | g7977 | g7977.t1 | exon | g7977.t1.exon3 | 27438560 | 27438710 |
| chr_2 | g7977 | g7977.t1 | cds | g7977.t1.CDS3 | 27438560 | 27438710 |
| chr_2 | g7977 | g7977.t1 | exon | g7977.t1.exon4 | 27438766 | 27439042 |
| chr_2 | g7977 | g7977.t1 | cds | g7977.t1.CDS4 | 27438766 | 27439042 |
| chr_2 | g7977 | g7977.t1 | exon | g7977.t1.exon5 | 27439111 | 27439260 |
| chr_2 | g7977 | g7977.t1 | cds | g7977.t1.CDS5 | 27439111 | 27439260 |
| chr_2 | g7977 | g7977.t1 | exon | g7977.t1.exon6 | 27439360 | 27439581 |
| chr_2 | g7977 | g7977.t1 | cds | g7977.t1.CDS6 | 27439360 | 27439581 |
| chr_2 | g7977 | g7977.t1 | exon | g7977.t1.exon7 | 27439659 | 27439850 |
| chr_2 | g7977 | g7977.t1 | cds | g7977.t1.CDS7 | 27439659 | 27439850 |
| chr_2 | g7977 | g7977.t1 | TSS | g7977.t1 | NA | NA |
| chr_2 | g7977 | g7977.t1 | TTS | g7977.t1 | NA | NA |
Sequences
>g7977.t1 Gene=g7977 Length=1836
ATGAGAGGCATACGAAACTCAATTAGTCTTCACAAATTTGCAACTTCTCCAAAAAATCGA
ACAGCGTATTTGTGTTTAGTGGCATCACAACAGCTTCACAATAATAATAATCAGATGTGC
TTAGCATCAGGCACTAATAACAGCAATAGTCCCGCTACAAACCTTTCACATGTTCGATAC
TTTCATTTAACACATATCTGTGATAAGTCGAATAAGGACCCAACAAATGGAAATGATAAA
AACAATAATAATTCGACAACATCAAGTGGTTCTAATAATAACAACAATAATAAAGACAAT
GGCAAAGACCCGAATAAAAAGAACACTCTTTCATGCCCAAAATGTGGCGATCCATGCACT
CATGTTGAAACTTTTGTAAATGCAACACGATTCGTCAAGTGTGAAAAATGTCATCATTTT
TTTGTGGTGCTTAGTGAGATGGACTCAAAAAAGACAGTCAAAGAAGAGTCTATTAAGGGA
ACAAAAAAACCACCGCCACCACCAAAAAAGATTATGGAATATTTGGACCGTCATGTAGTC
GGTCAAGAACTCGCCAAGAAGGTGCTATCAGTTGCAGTTTATAATCATTATAAACGCATT
TACCATAATTTGCCGCCACCATCAAATAACAATTCTACACAGTCAATTGATTCAATGGGA
AGAGGCAGTGATTTGTTGCATATTTCTGGCATAGGGCATACAATGCTTAGTTCAGCACCT
ACTGAAGTGCCACGTCCACCTTTATCGCCACCACAGCAACATCATCCTGGATCTGAATTA
TTAGAAGAAAAAAACCATACATTGAAATTAGAGAAAAGTAACATTTTAATGCTCGGACCA
ACAGGATCGGGAAAAACTTTATTAGCACAAACTATAGCGAAATGTTTGGATGTTCCATTT
GCCATTTGTGACTGTACTACATTAACTCAAGCTGGATATGTCGGAGAGGATATAGAAAGT
GTTATTGCTAAATTACTTCAAGATGCTAATTATAGTGTTGAAAGAGCTCAAACTGGAATA
GTTTTCCTTGATGAAGTCGATAAAATCGGCGCTGTTCCAGGAATCCATCAACTTCGCGAT
GTAGGTGGTGAAGGTGTTCAGCAAGGCATGCTCAAAATGCTCGAAGGAACAATCGTTAAT
GTTCCGGAAAGAAATTCACCGCGTAAACTTCGCGGCGAATCTGTACAGGTTGATACTACA
AACATTTTGTTTGTTGCTTCTGGTGCTTACACAGGATTAGATCGTTTAATTGCAAGGCGT
TTAAACGAAAAGTACTTGGGTTTTGGTATGCCGGCAACTTCATCGGAAGGTCGTCGTGCA
GCTCAAGCTAGTGCAGCGCCAATGGACAATGATCAAGCAGAACGTGACGCCAACTTGAGA
AAAGTTCAAGCGAGAGATTTAGTCGAGTTCGGAATGATACCCGAATTTGTTGGACGTTTT
CCAGTTTTAGTTCCATTTCATTCGTTAGACATTGACATGCTAGTAAGAATATTGACCGAA
CCCAAGAATGCACTTGTACAACAATATCGTGCACTTCTCGGAATGGATCAAGTGGAACTC
ACATTCTCATCTGAAGCTTTAAAAGCTATCGCTAAATTGGCTATGGAACGTCAAACGGGA
GCAAGAGGATTAAGAGCTATAATGGAATCTTTGCTACTCGATCCGATGTTTGAAGTACCC
GGATCTGAAATTAAAGCTGTACATATAACAGAAGAGTGCGTGATGGGAAGTCCTGCAATT
TATATTCACCGTTCGAGTGCAACATCATCAGATCCAAACGAGACTAATAGCAGCAGTGAA
GAGGAAGAAAATAGAAAATATCGCGTAAAACAATGA
>g7977.t1 Gene=g7977 Length=611
MRGIRNSISLHKFATSPKNRTAYLCLVASQQLHNNNNQMCLASGTNNSNSPATNLSHVRY
FHLTHICDKSNKDPTNGNDKNNNNSTTSSGSNNNNNNKDNGKDPNKKNTLSCPKCGDPCT
HVETFVNATRFVKCEKCHHFFVVLSEMDSKKTVKEESIKGTKKPPPPPKKIMEYLDRHVV
GQELAKKVLSVAVYNHYKRIYHNLPPPSNNNSTQSIDSMGRGSDLLHISGIGHTMLSSAP
TEVPRPPLSPPQQHHPGSELLEEKNHTLKLEKSNILMLGPTGSGKTLLAQTIAKCLDVPF
AICDCTTLTQAGYVGEDIESVIAKLLQDANYSVERAQTGIVFLDEVDKIGAVPGIHQLRD
VGGEGVQQGMLKMLEGTIVNVPERNSPRKLRGESVQVDTTNILFVASGAYTGLDRLIARR
LNEKYLGFGMPATSSEGRRAAQASAAPMDNDQAERDANLRKVQARDLVEFGMIPEFVGRF
PVLVPFHSLDIDMLVRILTEPKNALVQQYRALLGMDQVELTFSSEALKAIAKLAMERQTG
ARGLRAIMESLLLDPMFEVPGSEIKAVHITEECVMGSPAIYIHRSSATSSDPNETNSSSE
EEENRKYRVKQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g7977.t1 | CDD | cd00009 | AAA | 272 | 424 | 3.09716E-16 |
| 6 | g7977.t1 | Gene3D | G3DSA:1.10.8.60 | - | 488 | 589 | 8.1E-38 |
| 10 | g7977.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 71 | 104 | - |
| 11 | g7977.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 76 | 99 | - |
| 12 | g7977.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 584 | 611 | - |
| 3 | g7977.t1 | PANTHER | PTHR48102:SF7 | ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX-LIKE, MITOCHONDRIAL | 93 | 604 | 2.0E-189 |
| 4 | g7977.t1 | PANTHER | PTHR48102 | ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX-LIKE, MITOCHONDRIAL-RELATED | 93 | 604 | 2.0E-189 |
| 1 | g7977.t1 | Pfam | PF07724 | AAA domain (Cdc48 subfamily) | 271 | 482 | 5.3E-39 |
| 2 | g7977.t1 | Pfam | PF10431 | C-terminal, D2-small domain, of ClpB protein | 489 | 560 | 4.9E-14 |
| 14 | g7977.t1 | ProSiteProfiles | PS51902 | ClpX zinc binding (ZB) domain profile. | 100 | 153 | 14.75 |
| 8 | g7977.t1 | SMART | SM00382 | AAA_5 | 271 | 423 | 5.0E-10 |
| 9 | g7977.t1 | SMART | SM01086 | ClpB_D2_small_2 | 489 | 582 | 3.7E-30 |
| 5 | g7977.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 166 | 574 | 1.09E-59 |
| 13 | g7977.t1 | TIGRFAM | TIGR00382 | clpX: ATP-dependent Clp protease, ATP-binding subunit ClpX | 262 | 576 | 2.7E-114 |
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:0006457 | protein folding | BP |
| GO:0005524 | ATP binding | MF |
| GO:0051082 | unfolded protein binding | MF |
| GO:0008270 | zinc ion binding | MF |
| GO:0046983 | protein dimerization activity | MF |
| GO:0016887 | ATP hydrolysis activity | MF |
KEGG
Orthology
- This transcript has been annotated with K03544 (ATP-dependent Clp protease ATP-binding subunit ClpX)
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.
