General information for g5172.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Peroxisomal carnitine O-octanoyltransferase.
Parent gene
- The parent gene g5172 is located on chr_2: 7433546..7435563 (+ 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 | g5172 | g5172.t1 | TSS | g5172.t1 | 7433382 | 7433382 |
| chr_2 | g5172 | g5172.t1 | isoform | g5172.t1 | 7433546 | 7435563 |
| chr_2 | g5172 | g5172.t1 | exon | g5172.t1.exon1 | 7433546 | 7433794 |
| chr_2 | g5172 | g5172.t1 | cds | g5172.t1.CDS1 | 7433546 | 7433794 |
| chr_2 | g5172 | g5172.t1 | TTS | g5172.t1 | 7433778 | 7433778 |
| chr_2 | g5172 | g5172.t1 | exon | g5172.t1.exon2 | 7433853 | 7434600 |
| chr_2 | g5172 | g5172.t1 | cds | g5172.t1.CDS2 | 7433853 | 7434600 |
| chr_2 | g5172 | g5172.t1 | exon | g5172.t1.exon3 | 7434662 | 7435086 |
| chr_2 | g5172 | g5172.t1 | cds | g5172.t1.CDS3 | 7434662 | 7435086 |
| chr_2 | g5172 | g5172.t1 | exon | g5172.t1.exon4 | 7435144 | 7435563 |
| chr_2 | g5172 | g5172.t1 | cds | g5172.t1.CDS4 | 7435144 | 7435563 |
Sequences
>g5172.t1 Gene=g5172 Length=1842
ATGAACCGTGAAAATTTATTTATTCTACCTGATGGTTCGCCATCGACATTTTCACGAGAT
GAAAGTTTAGAAAAATTGCCACTGCCTAAATTAGAAGACACTTTAGAGCGATATTATAAA
AATTTACTTCCATTTGGTGATGAAAATGAGTTGAAAAATTCAAGAAAAATTATTGAAGAA
TTTAAAAATGGTGTTGGTAAGAAATTGCACAAAATGTTGGAAGAAAAAGCAGCAAAAGAA
AAAAATTGGGTTGAAAAATTCTGGGAAGATTATGCTTATCATTCATTTCGACTTCCACTT
GCACCGTATTCATCGATGGTAATGCCATTTATGCTTAAATTAGTAGGAGTTGATGAGAGT
AGAGAAAATCGATTAAAGTCAATTGCTAGGGTAGCATTTTATTCTATGGAGTGTTGGAAT
TTACTTCGCAATGAAAAATTTCGACCTGCAATGAGTGTAGATGGAAAAATTGTATTTTCT
TCCGACCAGTTAAGAAGATTGTATAACACTGCACGAGTGCCAGGCGACTTAAAAGATGAA
ATAAATTGTTATTTCAAAACAAAAACAGAAGGTGAATGTTCTTCAAAAATTGTTGTCATT
GGAAAAGGAAAAATTTTCTATTTTGATGCGCTTCATGATGGTAAAATAGTTTCACCTCAA
GAATTTTTGCATGCATTGACATTGATCCGTGATAAAATTGAAAATGACAAATTTGAGCGT
GGCATTCCGATTTTAACATGTGATGAACGAACAAATTGGTCAAAAAATCGTAATCATCTT
AAAGAATTGTCACAAGAAAATGAAGAATTTTTAAAAATTATTGAATCGTCAGCTTTGGTT
ATTTCACTTGATGACAATGAACCAAGAGACGTCAGTGAATTATCACAAAAAACTTCAGTT
GGTGATCATTATTCACGTTGGCATGACAAATGTTCATCATTTGTTTCTTTTAAAAATGGA
AAAATTGGTTCAGTTGGAGAACATAGCTGTTTTGATGGAACAGCCAGTAATGCTCCTTAT
ATTTTATTGAGTTTCATGGAAGAATCAGAACCTGATTGGGATGAAAAATTGGAATTAAAA
ATTCTTCCTAAAGAAATAAAATTCAAAATTGACGATCATTTAAAGAGTGAAATTTTAAGA
GTTGAAGAATTCACAAAAGTTATTGAAAAATCTTTGATTGTTCGTTTTGAAGAATTTAGA
GATTTCGGTAAAAGTAAAATGAAGGAATTTAAAATTCATCCCGATTGTTTTGTACAAATG
GCTCTGCAACTTGCATATTATTTAAATATGAATGGAGAACTTGCACCAACTTATGAAACT
GCAACAATGAGAAGTTATTATCATGGAAGAACTGAGACAGTGAGATCATGTTCAATTGAA
GTTAAAGAATGGCTTGAAAAAATGTATGATGACAATGTTACCAACACAGAAAAAGTCAAA
CTTTTTAAAACAGCAGCAAATTCACAGTTTAAATTAATGAACGATGCTAGAAATGGCAAA
GGTTTCGATAGACACCTTTTTGCCCTTTGGTGCATTGCTTATGAAAATAATTTTCCTATT
CCTGAACTCTATAATGATCCACTCTATACAAAATCAGGAGGTGGTGGCAATTTTGTGCTT
TCAACATCAACATTGGGTTATTTTATCAATATTGGCTATGTTGCACCAATGATACAAGAT
GGATTCGGAATTTTTTATACAATACATGATGAAAAAGTTTGGATTGTTATTTCATCATAC
AGAGAAAGTGAAAAGACATCAAGTAAAAAGTTTTATGACTCATTTTCAAATGCAATGATT
GAAATTAAAGAAATGCTTGGGAATTTGCAAAATAAATTGTAA
>g5172.t1 Gene=g5172 Length=613
MNRENLFILPDGSPSTFSRDESLEKLPLPKLEDTLERYYKNLLPFGDENELKNSRKIIEE
FKNGVGKKLHKMLEEKAAKEKNWVEKFWEDYAYHSFRLPLAPYSSMVMPFMLKLVGVDES
RENRLKSIARVAFYSMECWNLLRNEKFRPAMSVDGKIVFSSDQLRRLYNTARVPGDLKDE
INCYFKTKTEGECSSKIVVIGKGKIFYFDALHDGKIVSPQEFLHALTLIRDKIENDKFER
GIPILTCDERTNWSKNRNHLKELSQENEEFLKIIESSALVISLDDNEPRDVSELSQKTSV
GDHYSRWHDKCSSFVSFKNGKIGSVGEHSCFDGTASNAPYILLSFMEESEPDWDEKLELK
ILPKEIKFKIDDHLKSEILRVEEFTKVIEKSLIVRFEEFRDFGKSKMKEFKIHPDCFVQM
ALQLAYYLNMNGELAPTYETATMRSYYHGRTETVRSCSIEVKEWLEKMYDDNVTNTEKVK
LFKTAANSQFKLMNDARNGKGFDRHLFALWCIAYENNFPIPELYNDPLYTKSGGGGNFVL
STSTLGYFINIGYVAPMIQDGFGIFYTIHDEKVWIVISSYRESEKTSSKKFYDSFSNAMI
EIKEMLGNLQNKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5172.t1 | Gene3D | G3DSA:3.30.559.40 | - | 23 | 602 | 0 |
| 6 | g5172.t1 | Gene3D | G3DSA:3.30.559.70 | - | 82 | 395 | 0 |
| 2 | g5172.t1 | PANTHER | PTHR22589:SF67 | PEROXISOMAL CARNITINE O-OCTANOYLTRANSFERASE | 15 | 608 | 0 |
| 3 | g5172.t1 | PANTHER | PTHR22589 | CARNITINE O-ACYLTRANSFERASE | 15 | 608 | 0 |
| 1 | g5172.t1 | Pfam | PF00755 | Choline/Carnitine o-acyltransferase | 23 | 603 | 0 |
| 4 | g5172.t1 | SUPERFAMILY | SSF52777 | CoA-dependent acyltransferases | 15 | 383 | 0 |
| 5 | g5172.t1 | SUPERFAMILY | SSF52777 | CoA-dependent acyltransferases | 396 | 607 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5172/g5172.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5172.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016746 | acyltransferase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K05940 (carnitine O-octanoyltransferase)
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