General information for g5595.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t2 | isoform | g5595.t2 | 10446534 | 10448950 |
| chr_2 | g5595 | g5595.t2 | exon | g5595.t2.exon1 | 10446534 | 10446650 |
| chr_2 | g5595 | g5595.t2 | exon | g5595.t2.exon2 | 10446754 | 10446937 |
| chr_2 | g5595 | g5595.t2 | cds | g5595.t2.CDS1 | 10446909 | 10446937 |
| chr_2 | g5595 | g5595.t2 | exon | g5595.t2.exon3 | 10448201 | 10448950 |
| chr_2 | g5595 | g5595.t2 | cds | g5595.t2.CDS2 | 10448201 | 10448588 |
| chr_2 | g5595 | g5595.t2 | TSS | g5595.t2 | 10448983 | 10448983 |
| chr_2 | g5595 | g5595.t2 | TTS | g5595.t2 | NA | NA |
Sequences
>g5595.t2 Gene=g5595 Length=1051
ATGAAAGTGTTGAGTGCAAGTCATTTTCCTTCGGTTCGTCATCGAATCGATGTACAATAT
GCTAGTATCGTAAGATTTCTGTCACAAAACAGAAACGATGATGGATATCAATATTTACAC
AAATCAAATATGCCAACATACTATTTCCAAAAGTCACTGCCTCGACTCCCTATTCCAAAA
ATTGAAAAAACCCTTTCAAGATATTTAGACGCCCAACGACCCTTGCTTTCTGATGAAGAA
TTTAAAAAAACACAAGATGCATGCAACAAATTTGTTAAATCAGGTATAAAGTCCACAAAA
CTTTTTATGATAAGGAAAAATAATTTATAAATGTCTCGATAGGTGGTTGGGAACTTCAAG
CAATGTTGAAAGAGAAGGATAAAGTGAATAAGCACACATCATATATCTCTGAGCCTTGGT
ACACAATGTATTTGAAGGATCGTGCACCATTGCCTGTCAATTATAATCCTGTATTAATAA
TGAAGCATGACACTAGACCTGAATACAATGATCAAGCTATTCGAACGGCAAATGTCATTA
TTAGTTCAATGCGATTTATGCGTTCCCTTAATGAAGAAGTGCTTGTACCAGAAATATATC
ATATGGATCCATCTAAAACAGACACTGAAGCATTTAGAGCAAAAATCATGCGTTTTCCAT
CATTTATAGCCACATATGCTGCCTATTACTATAAAGCTTATCCCCTAGATATGGTACAAT
TTCAGGGACTTTTTGCAGCTACTAGAATTCATGATTTAACTGACGTTATCAAAGCTTAAA
GTGAAAGAACTCTTGTTTACATGATGTGGTGCTTGGGTTTTAACAAATAAACTTTCTCCG
CTATACATGCGTGCGATGGTTAAAATGCTCTTTTGTTATAAAAAGTAATAAATTATTTTT
ACAAAGAAACTGTCTATTCATTGTCACAAATTTAATTAAATTCTCTCTCATTGATTGCCT
TATTTCATCGCACACTTGAAATAGCTCTTTACTTTTAGTTTCTTTAGCTCTTAATCGAAT
GTCATTTCTAACTTTTATAATCGAATTAACT
>g5595.t2 Gene=g5595 Length=138
MLKEKDKVNKHTSYISEPWYTMYLKDRAPLPVNYNPVLIMKHDTRPEYNDQAIRTANVII
SSMRFMRSLNEEVLVPEIYHMDPSKTDTEAFRAKIMRFPSFIATYAAYYYKAYPLDMVQF
QGLFAATRIHDLTDVIKA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5595.t2 | Gene3D | G3DSA:3.30.559.40 | - | 1 | 63 | 8e-07 |
| 5 | g5595.t2 | Gene3D | G3DSA:1.20.1280.180 | - | 67 | 114 | 0e+00 |
| 2 | g5595.t2 | PANTHER | PTHR22589 | CARNITINE O-ACYLTRANSFERASE | 2 | 131 | 0e+00 |
| 3 | g5595.t2 | PANTHER | PTHR22589:SF16 | CARNITINE O-PALMITOYLTRANSFERASE 2, MITOCHONDRIAL | 2 | 131 | 0e+00 |
| 1 | g5595.t2 | Pfam | PF00755 | Choline/Carnitine o-acyltransferase | 3 | 129 | 0e+00 |
| 4 | g5595.t2 | SUPERFAMILY | SSF52777 | CoA-dependent acyltransferases | 2 | 132 | 0e+00 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5595/g5595.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5595.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.
