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.t19 isoform g7977.t19 27438779 27439850
chr_2 g7977 g7977.t19 exon g7977.t19.exon1 27438779 27439042
chr_2 g7977 g7977.t19 cds g7977.t19.CDS1 27438878 27439042
chr_2 g7977 g7977.t19 exon g7977.t19.exon2 27439111 27439260
chr_2 g7977 g7977.t19 cds g7977.t19.CDS2 27439111 27439260
chr_2 g7977 g7977.t19 exon g7977.t19.exon3 27439360 27439581
chr_2 g7977 g7977.t19 cds g7977.t19.CDS3 27439360 27439581
chr_2 g7977 g7977.t19 exon g7977.t19.exon4 27439659 27439850
chr_2 g7977 g7977.t19 cds g7977.t19.CDS4 27439659 27439850
chr_2 g7977 g7977.t19 TSS g7977.t19 NA NA
chr_2 g7977 g7977.t19 TTS g7977.t19 NA NA

Sequences

>g7977.t19 Gene=g7977 Length=828
CAAACTGGAATAGTTTTCCTTGATGAAGTCGATAAAATCGGCGCTGTTCCAGGAATCCAT
CAACTTCGCGATGTAGGTGGTGAAGGTGTTCAGCAAGGCATGCTCAAAATGCTCGAAGGA
ACAATCGTTAATGTTCCGGAAAGAAATTCACCGCGTAAACTTCGCGGCGAATCTGTACAG
GTTGATACTACAAACATTTTGTTTGTTGCTTCTGGTGCTTACACAGGATTAGATCGTTTA
ATTGCAAGGCGTTTAAACGAAAAGTACTTGGGTTTTGGTATGCCGGCAACTTCATCGGAA
GGTCGTCGTGCAGCTCAAGCTAGTGCAGCGCCAATGGACAATGATCAAGCAGAACGTGAC
GCCAACTTGAGAAAAGTTCAAGCGAGAGATTTAGTCGAGTTCGGAATGATACCCGAATTT
GTTGGACGTTTTCCAGTTTTAGTTCCATTTCATTCGTTAGACATTGACATGCTAGTAAGA
ATATTGACCGAACCCAAGAATGCACTTGTACAACAATATCGTGCACTTCTCGGAATGGAT
CAAGTGGAACTCACATTCTCATCTGAAGCTTTAAAAGCTATCGCTAAATTGGCTATGGAA
CGTCAAACGGGAGCAAGAGGATTAAGAGCTATAATGGAATCTTTGCTACTCGATCCGATG
TTTGAAGTACCCGGATCTGAAATTAAAGCTGTACATATAACAGAAGAGTGCGTGATGGGA
AGTCCTGCAATTTATATTCACCGTTCGAGTGCAACATCATCAGATCCAAACGAGACTAAT
AGCAGCAGTGAAGAGGAAGAAAATAGAAAATATCGCGTAAAACAATGA

>g7977.t19 Gene=g7977 Length=242
MLKMLEGTIVNVPERNSPRKLRGESVQVDTTNILFVASGAYTGLDRLIARRLNEKYLGFG
MPATSSEGRRAAQASAAPMDNDQAERDANLRKVQARDLVEFGMIPEFVGRFPVLVPFHSL
DIDMLVRILTEPKNALVQQYRALLGMDQVELTFSSEALKAIAKLAMERQTGARGLRAIME
SLLLDPMFEVPGSEIKAVHITEECVMGSPAIYIHRSSATSSDPNETNSSSEEEENRKYRV
KQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g7977.t19 Gene3D G3DSA:3.40.50.300 - 1 117 6.4E-36
9 g7977.t19 Gene3D G3DSA:1.10.8.60 - 119 220 1.5E-38
7 g7977.t19 MobiDBLite mobidb-lite consensus disorder prediction 215 242 -
3 g7977.t19 PANTHER PTHR48102:SF7 ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX-LIKE, MITOCHONDRIAL 1 235 6.5E-85
4 g7977.t19 PANTHER PTHR48102 ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX-LIKE, MITOCHONDRIAL-RELATED 1 235 6.5E-85
1 g7977.t19 Pfam PF07724 AAA domain (Cdc48 subfamily) 1 113 3.4E-10
2 g7977.t19 Pfam PF10431 C-terminal, D2-small domain, of ClpB protein 120 191 9.9E-15
6 g7977.t19 SMART SM01086 ClpB_D2_small_2 120 213 3.7E-30
5 g7977.t19 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 1 205 6.38E-24

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: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.

Raw TPM values