General information for g5595.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Carnitine O-palmitoyltransferase 2, mitochondrial.
Parent gene
- The parent gene g5595 is located on chr_2: 10448950..10452059 (- 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 | g5595 | g5595.t3 | TTS | g5595.t3 | 10446715 | 10446715 |
| chr_2 | g5595 | g5595.t3 | isoform | g5595.t3 | 10446754 | 10448201 |
| chr_2 | g5595 | g5595.t3 | exon | g5595.t3.exon1 | 10446754 | 10448201 |
| chr_2 | g5595 | g5595.t3 | cds | g5595.t3.CDS1 | 10446909 | 10447697 |
| chr_2 | g5595 | g5595.t3 | TSS | g5595.t3 | 10448983 | 10448983 |
Sequences
>g5595.t3 Gene=g5595 Length=1448
CCTAAAAGAGATAAAGATGAAATTGTTAGATTCAAGGATGTGAGACATGTGTTAGTAACA
AGAAATGGTCACTTTTATTATGTTGAAGTGCTTGATTCTGATGGCAATATTCGTGATCCA
GAATTCATTTATTCACAAATTAAATATTTATTGACAATAAGTGAAGATCAAAATTCACAT
CCAATTGGTGCATTGACAACACAAAATAGAAGAATTTGGTGGAATGCGAGAGAGCATTTG
ATTTCATCGAGTGCGAAGAATGCTGACAACTTGAAAGCAATCGATTCAGCTCTGTTCTGT
ATTAATCTAGATGAAACCAAATATAACGAAGAAAATCCCGTTCCAGCTGTTAGAGATTTT
CTTTTTGATTCTTGTAAAAATCGTTGGTATGACAAATCATTGAGTGTGATAATTGATAAA
TCAGGAACCACTGGCGTCACATTTGAGCATTCGCCAACTGATGGTGTTTCTGTTTTGCGT
TATTTTAATGAAATTTATAAAGACATGAACAAATCATTTGTAGGACCTGAGACTAAACTT
GTAAAAGGTGTTGAAACAACTGTCAGAAAGCTTGACTTTGACATTGATGATAAATCAAAA
AATGATATTGAAACAGCAATAAGTGCTCATCAAAATGTAGTTGGATCAATTGATATGAAC
TTCCTTAAGTATCAAAAACTTAACAAAGTTGAATGTAAAAAGTACAAAATCAGTCCCGAT
TCAATTATGCAGTTAGGCTTTCAACTTGCTTATTACAGACAAAACAAGAAATTTGTTGCA
ACATATGAAAGCTGCTCAACTTCCGCATTCCGTCACGGCCGGACAGAAACGATGAGACCA
TGTACAATTGAAACAAAAGCATTTGTAGAAGCAATTGATGGTAAAAACAAACCGTCAAAT
AAACAATTACGTGCAATGCTGGATCAATGTTCAAAGAAACATAATCAGTTAACAAAAGAT
GCCGCAATGGGACAAGGTTTTGACCGACATTTATTTGCATTAAGAACAGCAGCAGAGAGA
GTGAGAATAGTTGATGACTTTGATATTTTTAAAGATCCAGCATATAAAAGAATCAATCAT
TATATTTTATCAACAAGCACTTTGACGAGCAATGGTTTACTTGCGGGAGGTTTTGGACCA
GTTGTAAAAGACGGTTATGGAATTGGTTATAATATTCAAGAAGAATTGCTTGGTTGTGTA
GTTAGTAATTATAAAAATGAAACAAATAGTAAAGAATTTCTCGAATGTTTAAAGAGTGCA
TACGATGATTTAACTGACGTTATCAAAGCTTAAAGTGAAAGAACTCTTGTTTACATGATG
TGGTGCTTGGGTTTTAACAAATAAACTTTCTCCGCTATACATGCGTGCGATGGTTAAAAT
GCTCTTTTGTTATAAAAAGTAATAAATTATTTTTACAAAGAAACTGTCTATTCATTGTCA
CAAATTTA
>g5595.t3 Gene=g5595 Length=262
MNKSFVGPETKLVKGVETTVRKLDFDIDDKSKNDIETAISAHQNVVGSIDMNFLKYQKLN
KVECKKYKISPDSIMQLGFQLAYYRQNKKFVATYESCSTSAFRHGRTETMRPCTIETKAF
VEAIDGKNKPSNKQLRAMLDQCSKKHNQLTKDAAMGQGFDRHLFALRTAAERVRIVDDFD
IFKDPAYKRINHYILSTSTLTSNGLLAGGFGPVVKDGYGIGYNIQEELLGCVVSNYKNET
NSKEFLECLKSAYDDLTDVIKA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5595.t3 | Coils | Coil | Coil | 132 | 152 | - |
| 5 | g5595.t3 | Gene3D | G3DSA:3.30.559.40 | - | 14 | 262 | 6.7E-76 |
| 2 | g5595.t3 | PANTHER | PTHR22589 | CARNITINE O-ACYLTRANSFERASE | 5 | 261 | 2.2E-98 |
| 3 | g5595.t3 | PANTHER | PTHR22589:SF16 | CARNITINE O-PALMITOYLTRANSFERASE 2, MITOCHONDRIAL | 5 | 261 | 2.2E-98 |
| 1 | g5595.t3 | Pfam | PF00755 | Choline/Carnitine o-acyltransferase | 17 | 256 | 1.1E-82 |
| 4 | g5595.t3 | SUPERFAMILY | SSF52777 | CoA-dependent acyltransferases | 49 | 261 | 6.12E-70 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5595/g5595.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5595.t3.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.
