General information for g16716.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Carnitine O-palmitoyltransferase 1, liver isoform.
Parent gene
- The parent gene g16716 is located on chr_4: 10646121..10649365 (+ 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_4 | g16716 | g16716.t1 | TSS | g16716.t1 | 10646114 | 10646114 |
| chr_4 | g16716 | g16716.t1 | isoform | g16716.t1 | 10646121 | 10649365 |
| chr_4 | g16716 | g16716.t1 | exon | g16716.t1.exon1 | 10646121 | 10646371 |
| chr_4 | g16716 | g16716.t1 | cds | g16716.t1.CDS1 | 10646121 | 10646371 |
| chr_4 | g16716 | g16716.t1 | exon | g16716.t1.exon2 | 10646434 | 10646612 |
| chr_4 | g16716 | g16716.t1 | cds | g16716.t1.CDS2 | 10646434 | 10646612 |
| chr_4 | g16716 | g16716.t1 | exon | g16716.t1.exon3 | 10646796 | 10647255 |
| chr_4 | g16716 | g16716.t1 | cds | g16716.t1.CDS3 | 10646796 | 10647255 |
| chr_4 | g16716 | g16716.t1 | exon | g16716.t1.exon4 | 10647604 | 10648078 |
| chr_4 | g16716 | g16716.t1 | cds | g16716.t1.CDS4 | 10647604 | 10648078 |
| chr_4 | g16716 | g16716.t1 | exon | g16716.t1.exon5 | 10648131 | 10648216 |
| chr_4 | g16716 | g16716.t1 | cds | g16716.t1.CDS5 | 10648131 | 10648216 |
| chr_4 | g16716 | g16716.t1 | exon | g16716.t1.exon6 | 10648372 | 10649036 |
| chr_4 | g16716 | g16716.t1 | cds | g16716.t1.CDS6 | 10648372 | 10649036 |
| chr_4 | g16716 | g16716.t1 | exon | g16716.t1.exon7 | 10649175 | 10649365 |
| chr_4 | g16716 | g16716.t1 | cds | g16716.t1.CDS7 | 10649175 | 10649365 |
| chr_4 | g16716 | g16716.t1 | TTS | g16716.t1 | 10649463 | 10649463 |
Sequences
>g16716.t1 Gene=g16716 Length=2307
ATGGCGGAAGCACATCAAGCCACGCATTATTCATCATCAAATATTCACCAACATACTGAA
ATCAACCATGATCAAGAAACTTTAGAATTGGTTTTAAGTTCTGGTGGACATTCTTGGAAA
ATAAAATCAGCAAATCGAATCAAAAATTTTATTTATCCAGCAAGAATTGAAATTTTATAT
GTGACAGTTGGAATAGCAATTGCTTTATATTTTAGTGAAATGCCTTTTGGATTTATAGAG
ATGAAGTCAAGTTCTTCAATAATTTTTGATATTTTTGCCTGCATTTTTATTGGTTTAATT
TTGTTTGCAATAATTTGTGTTTGTATGAAAGTGACAATGATGCTATTGTTGAGATACCAA
GGCTATATGTATGAGACAAGAGGAAGAAAAGTGAGCTTGAAGACGCAAATTTGGGCAATA
TTGATGAAAAGTTTTTTAAAGTTTAATCCACCACAACTTTATAGTTTTCAATCACTTCTT
CCTCGTTTATCTGTCCCACCATTAAAAGACACTATAAATCGTTACTTGCGCTCAGTTCGT
CCAATTTATGATGATGAAACTTACAATCGAATTGCGCAAGAAGCTCAAGATTTTCAAAAT
GGAATTGGCAAAAAACTTCAACGTTATTTAATTTTAAAAAGTTGGTGGGCAACAAATTAT
GTATCAGATTGGTGGGAAGAATTTATTTATTTGAAAAGTTCAACACCATTGATGGTAAAT
AGCAATGTTTTTAGTTCTGATCATATTTCAAGAGATACAACAATTCAATCAGCAAGAGCA
GCAAATGTTTGTTATTTATTTTTGCAATTTAGAAAAAGCATCGATGATCAAACTTTGAAA
CCAATTATGGCTAATAATTTAGTACCACTTTGTTCTACTCAATATCAACGTCTTTTCAAT
ACAACTCGAATTCCTGGTATTGATGGTGATAAGCTGATACATTTTGAGACTTCCGATCAT
ATCGCAGTTTTACATAAAGGTTGCTATTATAAAGTGACAATTTGTGTCAATGGTCGACTT
TTAAAACCAAGAGAAATTCAATATCAATTTGAGCAAATTATAAATTCAAATAATCAAACA
TCACATGGTGAAAAATATCTTGCATCATTGACAGCATGGGAAAGAACAAAATGGGCAACA
ACAAGAAATAAATATTTTTCAAATGGAATAAATAAAAAATCACTTGATATAATTGAAAGT
GCTGCTTTTGTTCTCAATCTTCATGATGGTCCTTACATTATGGAACTAGAAAATTTAGAA
CAACCTGAAGTACTCACTTATTATTGCACACAAAATTTCTATGGACGTATTTATGATTTT
TGGTTTGATAAAAGTTTTAATATTTGTTTTGGAACCAATGGAAGAATGGCTTTTAATGCT
GAACATGCTTGGGGTGACGCACCAGCTGTTTCAAGAATGCTTGAAGAATGTATGGTGTAT
GATATTAAAAGCTATGATGCACATGGAAATATAAAAGGAACAATGGAAATAAAACCACCA
CTTCCAGTTCGTCTTAATTGGGATTTTTCAGATCAAAATTTAATCAATACAATTGATGAA
GCTTATGGTGATGGTTTAAAACTAATCAGTGATCTTGATTATCAATGTGTTGTTCATGAT
GCTTTTGGTAAAGGTTTAATGAAAGCTTGCAAACTTTCACCTGATGCTTTTATTCAAATG
GCTTTACAACTTGCTTATTTTCGTGATTTTGGTCGATTTTCATTAACATATGAAGCTTCA
ATGACGAGACTTTTTAAAGATGGTCGAACTGAAACTGTTCGATCTTGTACAATTGAATCG
TGTGCTTGGGTAAAATCAATGGAAGATCCAAAAACTTCAATACAAGAAAGAGTTAAATTA
CTGCAAGAAGCATGCAAAAGACACCAAAAAGGCTACCTTGAAGCAATGACAGGAAAAGGA
GTTGATCGACATCTTTTTTGTCTTTATGTTGTGTCAAAATATCTCGAAATTGATTCACCA
TTTTTGAAAGAAGTGCTAAGTGAGCCTTGGAGATTATCAACAAGTCAAACACCACATGGA
CAAAGTGATTTTGTTGATTTGAAAAAATATCCGCAATTAAAAGGATGTGCTGGTGGTTTT
GGACCTGTTTCTAAAGATGGTTATGGAATTTCCTACATCATTTCTGGTGAAGACCGAATA
TACTTTCATGTATCTAGTTTTAAAAGTAGTCCTGTAACAAACACTGATCGATTTGGTAAG
CGAATAAGAAAAGCTCTCTGGGATATTAAAGAACTTGTTGAAAAATTCAATTCTGAACAA
GGAGACAAAAGAAATGGACATAAATAA
>g16716.t1 Gene=g16716 Length=768
MAEAHQATHYSSSNIHQHTEINHDQETLELVLSSGGHSWKIKSANRIKNFIYPARIEILY
VTVGIAIALYFSEMPFGFIEMKSSSSIIFDIFACIFIGLILFAIICVCMKVTMMLLLRYQ
GYMYETRGRKVSLKTQIWAILMKSFLKFNPPQLYSFQSLLPRLSVPPLKDTINRYLRSVR
PIYDDETYNRIAQEAQDFQNGIGKKLQRYLILKSWWATNYVSDWWEEFIYLKSSTPLMVN
SNVFSSDHISRDTTIQSARAANVCYLFLQFRKSIDDQTLKPIMANNLVPLCSTQYQRLFN
TTRIPGIDGDKLIHFETSDHIAVLHKGCYYKVTICVNGRLLKPREIQYQFEQIINSNNQT
SHGEKYLASLTAWERTKWATTRNKYFSNGINKKSLDIIESAAFVLNLHDGPYIMELENLE
QPEVLTYYCTQNFYGRIYDFWFDKSFNICFGTNGRMAFNAEHAWGDAPAVSRMLEECMVY
DIKSYDAHGNIKGTMEIKPPLPVRLNWDFSDQNLINTIDEAYGDGLKLISDLDYQCVVHD
AFGKGLMKACKLSPDAFIQMALQLAYFRDFGRFSLTYEASMTRLFKDGRTETVRSCTIES
CAWVKSMEDPKTSIQERVKLLQEACKRHQKGYLEAMTGKGVDRHLFCLYVVSKYLEIDSP
FLKEVLSEPWRLSTSQTPHGQSDFVDLKKYPQLKGCAGGFGPVSKDGYGISYIISGEDRI
YFHVSSFKSSPVTNTDRFGKRIRKALWDIKELVEKFNSEQGDKRNGHK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g16716.t1 | Gene3D | G3DSA:3.30.559.40 | - | 160 | 749 | 8.7E-196 |
| 8 | g16716.t1 | Gene3D | G3DSA:3.30.559.70 | - | 219 | 535 | 8.7E-196 |
| 2 | g16716.t1 | PANTHER | PTHR22589:SF31 | CARNITINE PALMITOYLTRANSFERASE I | 65 | 754 | 5.9E-263 |
| 3 | g16716.t1 | PANTHER | PTHR22589 | CARNITINE O-ACYLTRANSFERASE | 65 | 754 | 5.9E-263 |
| 1 | g16716.t1 | Pfam | PF00755 | Choline/Carnitine o-acyltransferase | 160 | 750 | 1.1E-184 |
| 11 | g16716.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 49 | - |
| 14 | g16716.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 50 | 72 | - |
| 12 | g16716.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 73 | 86 | - |
| 13 | g16716.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 87 | 117 | - |
| 10 | g16716.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 118 | 768 | - |
| 7 | g16716.t1 | SUPERFAMILY | SSF52777 | CoA-dependent acyltransferases | 152 | 522 | 7.23E-107 |
| 6 | g16716.t1 | SUPERFAMILY | SSF52777 | CoA-dependent acyltransferases | 531 | 758 | 1.83E-76 |
| 5 | g16716.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 50 | 72 | - |
| 4 | g16716.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 87 | 109 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
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