Gene loci information

Transcript annotation

  • This transcript has been annotated as Peroxisomal carnitine O-octanoyltransferase.

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 g5171 g5171.t1 TSS g5171.t1 7430901 7430901
chr_2 g5171 g5171.t1 isoform g5171.t1 7431127 7433183
chr_2 g5171 g5171.t1 exon g5171.t1.exon1 7431127 7431164
chr_2 g5171 g5171.t1 cds g5171.t1.CDS1 7431127 7431164
chr_2 g5171 g5171.t1 exon g5171.t1.exon2 7431222 7431474
chr_2 g5171 g5171.t1 cds g5171.t1.CDS2 7431222 7431474
chr_2 g5171 g5171.t1 exon g5171.t1.exon3 7431530 7432705
chr_2 g5171 g5171.t1 cds g5171.t1.CDS3 7431530 7432705
chr_2 g5171 g5171.t1 exon g5171.t1.exon4 7432764 7433183
chr_2 g5171 g5171.t1 cds g5171.t1.CDS4 7432764 7433183
chr_2 g5171 g5171.t1 TTS g5171.t1 7433778 7433778

Sequences

>g5171.t1 Gene=g5171 Length=1887
ATGAAAAATCAACAAATCACAAATCTTCGTCATCTTGGAATTCTGAGTCGAGAAAGTCAA
TACATTTTACCTGATGGTTCTCCATCGACATTTTCACGAGATGAAAGTTTAGAAAAATTG
CCACTGCCTAAATTAGAAGACACTTTAGAGCGATATTATAAAAATTTACTGCCATTTGGT
GATGAAAATGAGTTGAAAAATTCAAGAAAAATTATTGAAGAATTTAAAAATGGTGTTGGT
AAGGAATTGCACAAAATGTTGGAAGAAAAAGCAGCAAAAGAAAAAAATTGGGTAAGAAAA
TTTTGGGAAGATTATGCCTATCTTGAATACCGAACTCCACTGGCACCTTTTAGTGTTCAA
ATTCAACCAATCATGCTGCAATCGATTGGAATTGAAGAAAGCAAGAAAGATTGTCTTAAA
AATTTCGCTCGCATTGTTCACTATTTTGGTGTGTATTTTCAAATTTTAAGAGAAGAAAAA
CTTCGTCCAACAACAAATCCAGATGGCAGTGTTGTTTTTTCATCTAATCAATTTAAAAGA
CTCTACAACACTTCAAGAATTCCAGGAGAGATTAAAGATGAAATTTTTAATTGTTTTAAA
ACAAAGACTGAAGGTGAATGTCCATCGACAATTGTTGTCATTGGAAAAGGTAGAATTTTC
TACTTTGATATAATTCAAAATAATAAACTGTTGTCACCTGCTGAATTATTGCACACATTT
TCAATAATTTATGGAAAAATTGACAATGAAAGTGAAAATTATTCAATTCCTTTACTGACT
TGTGACGAAAGAACTGGTTGGTTTAAAAATAGAAAACATTTGATTGAAATTTCTAATGAA
AATGAAGAATTTTTAAAAGTCATTGAAAGTTCAATGATGGTTTTTATACTTGATGATCGT
GAACCAAGAGACATCTCTGAAGTATGTGCGCATCTTTTAGATGGAAATTATCAATCAAAA
TGGATCGATAAATCAGTTTCATTGACAGTATTTAGAAATGGAAAATATGGTTGTGTTGGT
GAACACAGTTCTTATGATGGTCCAGTCTCTATGAGTTATGGTGGTTTTATTTTAGAAAGT
TTCACAGAAGATCCAGAACCAAATTGGAATGAAAATTTAAAATACAAAATTCTTCCTAAA
GAAATAAAATTCAAAATTGATGAAAAAATCAAAAGTGAAATTGCAAGAGTAGAAAAAGTT
GTAGAAGGTTTTACAGACTCTGTAACAGTTTATTGTCAAGAATATCGGAATTATGGAAAA
AACTTTATGAAATTACAAAAAATTCATCCCGATTGTTTTGTGCAAATGGCTCTGCAGCTT
GCATATTTTAAAATACATCAAAAACTGGCACCAACTTATGAAACTGCAACAATGAGAAGT
TATTATCATGGAAGAACTGAGACAGTGAGATCATGTTCAATTGAAGTCAAAGAATGGCTT
GAGAAAATGTATGATGACAAAGCTAGCAACACAGAAAAAGTCAAACTTTTTAAAACAGCA
GCAAATTCACAGTTTAAATTAATGAACGATGCGAGAAGTGGCAAAGGATTTGATAGACAT
TTATTTGCTATGTGGTGCATTGCACGTGAAAATAACATTCAAATTCCACAACTTTATAGT
GATCCATTATATTTTAAATCGGGTGGTGGTGGCAATTTTTATTTATCGACATCAACCTTA
GGCTATTCAATATGCAATGGATGTGTTGCACCAATGTTAACTGACGGTTATGGAGTATTT
TATACAATGCTCGATAATTTTGTATGGATCATTATAACTGCATTTAGAGAAAGTAAAGTA
ACATCGAGCAAAAAATTTTATGAAGCATTTGAGAGTGCAATGAATGAAATCAGTCAACTT
TTAGAAGCTACAAATTCTAAACTTTAA

>g5171.t1 Gene=g5171 Length=628
MKNQQITNLRHLGILSRESQYILPDGSPSTFSRDESLEKLPLPKLEDTLERYYKNLLPFG
DENELKNSRKIIEEFKNGVGKELHKMLEEKAAKEKNWVRKFWEDYAYLEYRTPLAPFSVQ
IQPIMLQSIGIEESKKDCLKNFARIVHYFGVYFQILREEKLRPTTNPDGSVVFSSNQFKR
LYNTSRIPGEIKDEIFNCFKTKTEGECPSTIVVIGKGRIFYFDIIQNNKLLSPAELLHTF
SIIYGKIDNESENYSIPLLTCDERTGWFKNRKHLIEISNENEEFLKVIESSMMVFILDDR
EPRDISEVCAHLLDGNYQSKWIDKSVSLTVFRNGKYGCVGEHSSYDGPVSMSYGGFILES
FTEDPEPNWNENLKYKILPKEIKFKIDEKIKSEIARVEKVVEGFTDSVTVYCQEYRNYGK
NFMKLQKIHPDCFVQMALQLAYFKIHQKLAPTYETATMRSYYHGRTETVRSCSIEVKEWL
EKMYDDKASNTEKVKLFKTAANSQFKLMNDARSGKGFDRHLFAMWCIARENNIQIPQLYS
DPLYFKSGGGGNFYLSTSTLGYSICNGCVAPMLTDGYGVFYTMLDNFVWIIITAFRESKV
TSSKKFYEAFESAMNEISQLLEATNSKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g5171.t1 Gene3D G3DSA:3.30.559.40 - 37 617 1.6E-169
6 g5171.t1 Gene3D G3DSA:3.30.559.70 - 96 411 1.6E-169
2 g5171.t1 PANTHER PTHR22589:SF67 PEROXISOMAL CARNITINE O-OCTANOYLTRANSFERASE 29 625 1.3E-173
3 g5171.t1 PANTHER PTHR22589 CARNITINE O-ACYLTRANSFERASE 29 625 1.3E-173
1 g5171.t1 Pfam PF00755 Choline/Carnitine o-acyltransferase 37 617 5.7E-163
9 g5171.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 575 -
10 g5171.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 576 595 -
8 g5171.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 596 628 -
5 g5171.t1 SUPERFAMILY SSF52777 CoA-dependent acyltransferases 29 401 3.11E-96
4 g5171.t1 SUPERFAMILY SSF52777 CoA-dependent acyltransferases 408 622 1.56E-73

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5171/g5171.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5171.t1.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0016746 acyltransferase 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. There were no conditions that were differentially expressed