Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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 g5172 g5172.t2 TSS g5172.t2 7433382 7433382
chr_2 g5172 g5172.t2 isoform g5172.t2 7433546 7434598
chr_2 g5172 g5172.t2 exon g5172.t2.exon1 7433546 7433794
chr_2 g5172 g5172.t2 cds g5172.t2.CDS1 7433546 7433794
chr_2 g5172 g5172.t2 exon g5172.t2.exon2 7433853 7434598
chr_2 g5172 g5172.t2 cds g5172.t2.CDS2 7433853 7434596
chr_2 g5172 g5172.t2 TTS g5172.t2 NA NA

Sequences

>g5172.t2 Gene=g5172 Length=995
ATGAACCGTGAAAATTTATTTATTCTACCTGATGGTTCGCCATCGACATTTTCACGAGAT
GAAAGTTTAGAAAAATTGCCACTGCCTAAATTAGAAGACACTTTAGAGCGATATTATAAA
AATTTACTTCCATTTGGTGATGAAAATGAGTTGAAAAATTCAAGAAAAATTATTGAAGAA
TTTAAAAATGGTGTTGGTAAGAAATTGCACAAAATGTTGGAAGAAAAAGCAGCAAAAGAA
AAAAATTGGGTTGAAAAATTCTGGGAAGATTATGCTTATCATTCATTTCGACTTCCACTT
GCACCGTATTCATCGATGGTAATGCCATTTATGCTTAAATTAGTAGGAGTTGATGAGAGT
AGAGAAAATCGATTAAAGTCAATTGCTAGGGTAGCATTTTATTCTATGGAGTGTTGGAAT
TTACTTCGCAATGAAAAATTTCGACCTGCAATGAGTGTAGATGGAAAAATTGTATTTTCT
TCCGACCAGTTAAGAAGATTGTATAACACTGCACGAGTGCCAGGCGACTTAAAAGATGAA
ATAAATTGTTATTTCAAAACAAAAACAGAAGGTGAATGTTCTTCAAAAATTGTTGTCATT
GGAAAAGGAAAAATTTTCTATTTTGATGCGCTTCATGATGGTAAAATAGTTTCACCTCAA
GAATTTTTGCATGCATTGACATTGATCCGTGATAAAATTGAAAATGACAAATTTGAGCGT
GGCATTCCGATTTTAACATGTGATGAACGAACAAATTGGTCAAAAAATCGTAATCATCTT
AAAGAATTGTCACAAGAAAATGAAGAATTTTTAAAAATTATTGAATCGTCAGCTTTGGTT
ATTTCACTTGATGACAATGAACCAAGAGACGTCAGTGAATTATCACAAAAAACTTCAGTT
GGTGATCATTATTCACGTTGGCATGACAAATGTTCATCATTTGTTTCTTTTAAAAATGGA
AAAATTGGTTCAGTTGGAGAACATAGCTGTTTTGA

>g5172.t2 Gene=g5172 Length=331
MNRENLFILPDGSPSTFSRDESLEKLPLPKLEDTLERYYKNLLPFGDENELKNSRKIIEE
FKNGVGKKLHKMLEEKAAKEKNWVEKFWEDYAYHSFRLPLAPYSSMVMPFMLKLVGVDES
RENRLKSIARVAFYSMECWNLLRNEKFRPAMSVDGKIVFSSDQLRRLYNTARVPGDLKDE
INCYFKTKTEGECSSKIVVIGKGKIFYFDALHDGKIVSPQEFLHALTLIRDKIENDKFER
GIPILTCDERTNWSKNRNHLKELSQENEEFLKIIESSALVISLDDNEPRDVSELSQKTSV
GDHYSRWHDKCSSFVSFKNGKIGSVGEHSCF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g5172.t2 Gene3D G3DSA:3.30.559.40 - 23 81 0
5 g5172.t2 Gene3D G3DSA:3.30.559.70 - 82 330 0
2 g5172.t2 PANTHER PTHR22589:SF67 PEROXISOMAL CARNITINE O-OCTANOYLTRANSFERASE 15 331 0
3 g5172.t2 PANTHER PTHR22589 CARNITINE O-ACYLTRANSFERASE 15 331 0
1 g5172.t2 Pfam PF00755 Choline/Carnitine o-acyltransferase 23 330 0
4 g5172.t2 SUPERFAMILY SSF52777 CoA-dependent acyltransferases 15 330 0

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5172/g5172.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5172.t2.fa.iupred3.txt does not exist

GO terms from InterProScan

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