Gene loci information

Transcript annotation

  • This transcript has been annotated as ATP-dependent Clp protease ATP-binding subunit clpX-like, 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_2 g7977 g7977.t15 isoform g7977.t15 27437720 27439850
chr_2 g7977 g7977.t15 exon g7977.t15.exon1 27437720 27438498
chr_2 g7977 g7977.t15 cds g7977.t15.CDS1 27437769 27438498
chr_2 g7977 g7977.t15 exon g7977.t15.exon2 27438560 27438710
chr_2 g7977 g7977.t15 cds g7977.t15.CDS2 27438560 27438710
chr_2 g7977 g7977.t15 exon g7977.t15.exon3 27438766 27439042
chr_2 g7977 g7977.t15 cds g7977.t15.CDS3 27438766 27439042
chr_2 g7977 g7977.t15 exon g7977.t15.exon4 27439111 27439260
chr_2 g7977 g7977.t15 cds g7977.t15.CDS4 27439111 27439260
chr_2 g7977 g7977.t15 exon g7977.t15.exon5 27439360 27439581
chr_2 g7977 g7977.t15 cds g7977.t15.CDS5 27439360 27439581
chr_2 g7977 g7977.t15 exon g7977.t15.exon6 27439659 27439850
chr_2 g7977 g7977.t15 cds g7977.t15.CDS6 27439659 27439850
chr_2 g7977 g7977.t15 TSS g7977.t15 NA NA
chr_2 g7977 g7977.t15 TTS g7977.t15 NA NA

Sequences

>g7977.t15 Gene=g7977 Length=1771
GTATTTGTGTTTAGTGGCATCACAACAGCTTCACAATAATAATAATCAGATGTGCTTAGC
ATCAGGCACTAATAACAGCAATAGTCCCGCTACAAACCTTTCACATGTTCGATACTTTCA
TTTAACACATATCTGTGATAAGTCGAATAAGGACCCAACAAATGGAAATGATAAAAACAA
TAATAATTCGACAACATCAAGTGGTTCTAATAATAACAACAATAATAAAGACAATGGCAA
AGACCCGAATAAAAAGAACACTCTTTCATGCCCAAAATGTGGCGATCCATGCACTCATGT
TGAAACTTTTGTAAATGCAACACGATTCGTCAAGTGTGAAAAATGTCATCATTTTTTTGT
GGTGCTTAGTGAGATGGACTCAAAAAAGACAGTCAAAGAAGAGTCTATTAAGGGAACAAA
AAAACCACCGCCACCACCAAAAAAGATTATGGAATATTTGGACCGTCATGTAGTCGGTCA
AGAACTCGCCAAGAAGGTGCTATCAGTTGCAGTTTATAATCATTATAAACGCATTTACCA
TAATTTGCCGCCACCATCAAATAACAATTCTACACAGTCAATTGATTCAATGGGAAGAGG
CAGTGATTTGTTGCATATTTCTGGCATAGGGCATACAATGCTTAGTTCAGCACCTACTGA
AGTGCCACGTCCACCTTTATCGCCACCACAGCAACATCATCCTGGATCTGAATTATTAGA
AGAAAAAAACCATACATTGAAATTAGAGAAAAGTAACATTTTAATGCTCGGACCAACAGG
ATCGGGAAAAACTTTATTAGCACAAACTATAGCGAAATGTTTGGATGTTCCATTTGCCAT
TTGTGACTGTACTACATTAACTCAAGCTGGATATGTCGGAGAGGATATAGAAAGTGTTAT
TGCTAAATTACTTCAAGATGCTAATTATAGTGTTGAAAGAGCTCAAACTGGAATAGTTTT
CCTTGATGAAGTCGATAAAATCGGCGCTGTTCCAGGAATCCATCAACTTCGCGATGTAGG
TGGTGAAGGTGTTCAGCAAGGCATGCTCAAAATGCTCGAAGGAACAATCGTTAATGTTCC
GGAAAGAAATTCACCGCGTAAACTTCGCGGCGAATCTGTACAGGTTGATACTACAAACAT
TTTGTTTGTTGCTTCTGGTGCTTACACAGGATTAGATCGTTTAATTGCAAGGCGTTTAAA
CGAAAAGTACTTGGGTTTTGGTATGCCGGCAACTTCATCGGAAGGTCGTCGTGCAGCTCA
AGCTAGTGCAGCGCCAATGGACAATGATCAAGCAGAACGTGACGCCAACTTGAGAAAAGT
TCAAGCGAGAGATTTAGTCGAGTTCGGAATGATACCCGAATTTGTTGGACGTTTTCCAGT
TTTAGTTCCATTTCATTCGTTAGACATTGACATGCTAGTAAGAATATTGACCGAACCCAA
GAATGCACTTGTACAACAATATCGTGCACTTCTCGGAATGGATCAAGTGGAACTCACATT
CTCATCTGAAGCTTTAAAAGCTATCGCTAAATTGGCTATGGAACGTCAAACGGGAGCAAG
AGGATTAAGAGCTATAATGGAATCTTTGCTACTCGATCCGATGTTTGAAGTACCCGGATC
TGAAATTAAAGCTGTACATATAACAGAAGAGTGCGTGATGGGAAGTCCTGCAATTTATAT
TCACCGTTCGAGTGCAACATCATCAGATCCAAACGAGACTAATAGCAGCAGTGAAGAGGA
AGAAAATAGAAAATATCGCGTAAAACAATGA

>g7977.t15 Gene=g7977 Length=573
MCLASGTNNSNSPATNLSHVRYFHLTHICDKSNKDPTNGNDKNNNNSTTSSGSNNNNNNK
DNGKDPNKKNTLSCPKCGDPCTHVETFVNATRFVKCEKCHHFFVVLSEMDSKKTVKEESI
KGTKKPPPPPKKIMEYLDRHVVGQELAKKVLSVAVYNHYKRIYHNLPPPSNNNSTQSIDS
MGRGSDLLHISGIGHTMLSSAPTEVPRPPLSPPQQHHPGSELLEEKNHTLKLEKSNILML
GPTGSGKTLLAQTIAKCLDVPFAICDCTTLTQAGYVGEDIESVIAKLLQDANYSVERAQT
GIVFLDEVDKIGAVPGIHQLRDVGGEGVQQGMLKMLEGTIVNVPERNSPRKLRGESVQVD
TTNILFVASGAYTGLDRLIARRLNEKYLGFGMPATSSEGRRAAQASAAPMDNDQAERDAN
LRKVQARDLVEFGMIPEFVGRFPVLVPFHSLDIDMLVRILTEPKNALVQQYRALLGMDQV
ELTFSSEALKAIAKLAMERQTGARGLRAIMESLLLDPMFEVPGSEIKAVHITEECVMGSP
AIYIHRSSATSSDPNETNSSSEEEENRKYRVKQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g7977.t15 CDD cd00009 AAA 234 386 3.19186E-16
6 g7977.t15 Gene3D G3DSA:1.10.8.60 - 450 551 7.3E-38
12 g7977.t15 MobiDBLite mobidb-lite consensus disorder prediction 33 66 -
10 g7977.t15 MobiDBLite mobidb-lite consensus disorder prediction 38 61 -
11 g7977.t15 MobiDBLite mobidb-lite consensus disorder prediction 546 573 -
3 g7977.t15 PANTHER PTHR48102:SF7 ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX-LIKE, MITOCHONDRIAL 55 566 1.7E-189
4 g7977.t15 PANTHER PTHR48102 ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX-LIKE, MITOCHONDRIAL-RELATED 55 566 1.7E-189
1 g7977.t15 Pfam PF07724 AAA domain (Cdc48 subfamily) 233 444 4.7E-39
2 g7977.t15 Pfam PF10431 C-terminal, D2-small domain, of ClpB protein 451 522 4.4E-14
14 g7977.t15 ProSiteProfiles PS51902 ClpX zinc binding (ZB) domain profile. 62 115 14.75
8 g7977.t15 SMART SM00382 AAA_5 233 385 5.0E-10
9 g7977.t15 SMART SM01086 ClpB_D2_small_2 451 544 3.7E-30
5 g7977.t15 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 128 536 9.14E-60
13 g7977.t15 TIGRFAM TIGR00382 clpX: ATP-dependent Clp protease, ATP-binding subunit ClpX 224 538 2.5E-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

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.

Raw TPM values