General information for g7977.t16
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.t16 | isoform | g7977.t16 | 27437728 | 27438700 |
| chr_2 | g7977 | g7977.t16 | exon | g7977.t16.exon1 | 27437728 | 27438498 |
| chr_2 | g7977 | g7977.t16 | cds | g7977.t16.CDS1 | 27437769 | 27438498 |
| chr_2 | g7977 | g7977.t16 | exon | g7977.t16.exon2 | 27438560 | 27438700 |
| chr_2 | g7977 | g7977.t16 | cds | g7977.t16.CDS2 | 27438560 | 27438699 |
| chr_2 | g7977 | g7977.t16 | TSS | g7977.t16 | NA | NA |
| chr_2 | g7977 | g7977.t16 | TTS | g7977.t16 | NA | NA |
Sequences
>g7977.t16 Gene=g7977 Length=912
GTTTAGTGGCATCACAACAGCTTCACAATAATAATAATCAGATGTGCTTAGCATCAGGCA
CTAATAACAGCAATAGTCCCGCTACAAACCTTTCACATGTTCGATACTTTCATTTAACAC
ATATCTGTGATAAGTCGAATAAGGACCCAACAAATGGAAATGATAAAAACAATAATAATT
CGACAACATCAAGTGGTTCTAATAATAACAACAATAATAAAGACAATGGCAAAGACCCGA
ATAAAAAGAACACTCTTTCATGCCCAAAATGTGGCGATCCATGCACTCATGTTGAAACTT
TTGTAAATGCAACACGATTCGTCAAGTGTGAAAAATGTCATCATTTTTTTGTGGTGCTTA
GTGAGATGGACTCAAAAAAGACAGTCAAAGAAGAGTCTATTAAGGGAACAAAAAAACCAC
CGCCACCACCAAAAAAGATTATGGAATATTTGGACCGTCATGTAGTCGGTCAAGAACTCG
CCAAGAAGGTGCTATCAGTTGCAGTTTATAATCATTATAAACGCATTTACCATAATTTGC
CGCCACCATCAAATAACAATTCTACACAGTCAATTGATTCAATGGGAAGAGGCAGTGATT
TGTTGCATATTTCTGGCATAGGGCATACAATGCTTAGTTCAGCACCTACTGAAGTGCCAC
GTCCACCTTTATCGCCACCACAGCAACATCATCCTGGATCTGAATTATTAGAAGAAAAAA
ACCATACATTGAAATTAGAGAAAAGTAACATTTTAATGCTCGGACCAACAGGATCGGGAA
AAACTTTATTAGCACAAACTATAGCGAAATGTTTGGATGTTCCATTTGCCATTTGTGACT
GTACTACATTAACTCAAGCTGGATATGTCGGAGAGGATATAGAAAGTGTTATTGCTAAAT
TACTTCAAGATG
>g7977.t16 Gene=g7977 Length=290
MCLASGTNNSNSPATNLSHVRYFHLTHICDKSNKDPTNGNDKNNNNSTTSSGSNNNNNNK
DNGKDPNKKNTLSCPKCGDPCTHVETFVNATRFVKCEKCHHFFVVLSEMDSKKTVKEESI
KGTKKPPPPPKKIMEYLDRHVVGQELAKKVLSVAVYNHYKRIYHNLPPPSNNNSTQSIDS
MGRGSDLLHISGIGHTMLSSAPTEVPRPPLSPPQQHHPGSELLEEKNHTLKLEKSNILML
GPTGSGKTLLAQTIAKCLDVPFAICDCTTLTQAGYVGEDIESVIAKLLQD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g7977.t16 | CDD | cd00009 | AAA | 234 | 289 | 3.6787E-9 |
| 6 | g7977.t16 | MobiDBLite | mobidb-lite | consensus disorder prediction | 33 | 66 | - |
| 5 | g7977.t16 | MobiDBLite | mobidb-lite | consensus disorder prediction | 38 | 61 | - |
| 2 | g7977.t16 | PANTHER | PTHR48102:SF7 | ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX-LIKE, MITOCHONDRIAL | 55 | 290 | 3.7E-68 |
| 3 | g7977.t16 | PANTHER | PTHR48102 | ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX-LIKE, MITOCHONDRIAL-RELATED | 55 | 290 | 3.7E-68 |
| 1 | g7977.t16 | Pfam | PF07724 | AAA domain (Cdc48 subfamily) | 233 | 289 | 3.0E-7 |
| 7 | g7977.t16 | ProSiteProfiles | PS51902 | ClpX zinc binding (ZB) domain profile. | 62 | 115 | 14.75 |
| 4 | g7977.t16 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 128 | 289 | 4.83E-23 |
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.
