Gene loci information

Transcript annotation

  • This transcript has been annotated as Carnitine O-palmitoyltransferase 1, liver isoform.

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_1 g14114 g14114.t1 TTS g14114.t1 34782424 34782424
chr_1 g14114 g14114.t1 isoform g14114.t1 34783400 34785686
chr_1 g14114 g14114.t1 exon g14114.t1.exon1 34783400 34784089
chr_1 g14114 g14114.t1 cds g14114.t1.CDS1 34783400 34784089
chr_1 g14114 g14114.t1 exon g14114.t1.exon2 34784147 34784291
chr_1 g14114 g14114.t1 cds g14114.t1.CDS2 34784147 34784291
chr_1 g14114 g14114.t1 exon g14114.t1.exon3 34784349 34785363
chr_1 g14114 g14114.t1 cds g14114.t1.CDS3 34784349 34785363
chr_1 g14114 g14114.t1 exon g14114.t1.exon4 34785428 34785686
chr_1 g14114 g14114.t1 cds g14114.t1.CDS4 34785428 34785686
chr_1 g14114 g14114.t1 TSS g14114.t1 34786310 34786310

Sequences

>g14114.t1 Gene=g14114 Length=2109
ATGTCTTATCCACTTTCACCGAACAGTTATTGGTTGATTTTTGGCATCTTCATTCCTTTC
TATTTTCCTCTTCAACAAGGCGATGTTTATTTAAAAGTGATAGGAAAAATGGCATTATAT
AGCTTTATTTTATGGATAAGATTGTGTGTGATTTGCCGATTTTTATTGACACTTGTGCTA
AAACATAAAGGACTGATTTTAGAAACAAGAGGGCAAAATCCAACTTTTAAGACTAAAATG
TATAAATATTTTCTTGAAAAACTTAAAGTCTGGAACAAACCACTCTTCTTTAGTTTTCAA
AATGCTCTACCTCGTTTGTCTGTACCCGATTTAAAAGTCACAATTAAAAAGTATTTAGAC
TCAATTCGAAGCTTTACTGATGATGAGAATTATGAAAGAATTAAAAAAGAAGCAGAAACT
TTCGAGAATGGACTTGGAAAGAAAATTCAAAGAAAATTGGTTTTTAAAAGTTGGAAAAGT
GAAAACTATGTCAGTGATTGGTGGGAAGAATATCACTATCTAAAAAGTCGTGCAGCTCTA
ATGTATGGAACAAGTATTTATTTAACTGACAATATAAATCAAGTGACAACAAGTCAATCA
GCAAGGGCAGCAAACTTAATCAATTTAATGTTAAAATTTAGAGACAAAATTCTTCGACAA
GAATTGGAACCAATTTATTTGAGAAATTTATTGCCAATTTGTGTTGCACAATATGAAAGA
CTTTTCAATACAGCTCGAATTCCAGGAATTGAAAGTGATAAAATTATTCACGTTGAAGAT
TCAAAGCACGTTGTGGTGATGCATAAAGGATCTTATTATAAACTTAATGTTTATTATCGT
GAACATATGCTCAATGCAGCTGATTTGCAATACCAAATTGAAGAAATTTTACAACTCAAA
CCAACAACATCATCAACTGAGAAACATTTACCATCATTGACTGCTTGGAATCGTACTAAA
TGGGCAGAAGTTCGAGATAAATTTTTCTCAACTGGAATCAATAAAGAATCTTTAGAAGCA
ATTGAAAGTGCAGCATTTATAATTGCATTAGATGATGAGCCTTATATTTTTGACCTTAAA
TCATCACCAGAAGAGTATGGTCATTATGGAAAGCAATTGCTTGTTGGAAATGGTCACAAT
CGTTGGTTTGACAAGAGTTTCAATTTATGTGTTGGAAGTAATGGACGAGTTGGTTTACTT
AATGAGCATACTTATGGTGATGGTTCTGTTGCTGCACATTTCTTTGAAGAATGTCTTATT
GATGATTATCATTGTTATGATAAAGAAGGAAAATTAAAAGTCAAAGTTGAAAATAAGTCA
TCATTGCCAAAACCAGAAAAGCTTGAATGGAGTTTAATTGATATAGATTTAATTGATGCT
GTTGAAAAAGCACATGAAGATGTTATGAATGTTGTTAATAACGTTGACCATCAAATAAAA
TTACACAAATCGTTTGGTCGTGGATTTATGAAAAAATGTAAAGTTTCACCTGATGCATTT
ATTCAAATGGCAGTACAACTTGCGTATTATCGACAACATCAAAAGTTCTCATTAACTTAT
GAGCCAGCGATGACGAGACTTTTTAAGAAAGGTCGAACTGAGACAATTAGATCATGCACA
ATTGAATCTTCAACTTGGGCAAAGTCAATGGATAATAAAAATTCTATAAAAGAAGAAAAA
TTAAAATTATTCAAGAAAGCTTGTGAAAAACATCAACAAATGTATTTGGACGCAATGTTT
GGAAATGGCGTTGATCGTCATTTATTTGCATTACAAACAGCAGCTAAATTAAATGGTAGT
GAATCCAATTTCCTCAATGAAGCTTGCAATGAACCATTTATGATGTTAACAAGTCACATT
CCACACGCTCAAAGTCCAAAGTCAAATCATGATAATGTCAAAGATTTTTTCATTACAGCA
GGTGCTGCAATGCCCCCAGGAATACACAAAGGCTACAGCATCTCTTATTTTCCATTTGAT
GATGAACTTTTATTTTTCCATGTTTCAAGTATGAAAAATTGCAATTCAACTGATACGACA
AAATTATTAAATGGCATTTTTCAAGCATTAACAGATATCAAAAATTTATTTGTAGAGAAT
GAAAAATAA

>g14114.t1 Gene=g14114 Length=702
MSYPLSPNSYWLIFGIFIPFYFPLQQGDVYLKVIGKMALYSFILWIRLCVICRFLLTLVL
KHKGLILETRGQNPTFKTKMYKYFLEKLKVWNKPLFFSFQNALPRLSVPDLKVTIKKYLD
SIRSFTDDENYERIKKEAETFENGLGKKIQRKLVFKSWKSENYVSDWWEEYHYLKSRAAL
MYGTSIYLTDNINQVTTSQSARAANLINLMLKFRDKILRQELEPIYLRNLLPICVAQYER
LFNTARIPGIESDKIIHVEDSKHVVVMHKGSYYKLNVYYREHMLNAADLQYQIEEILQLK
PTTSSTEKHLPSLTAWNRTKWAEVRDKFFSTGINKESLEAIESAAFIIALDDEPYIFDLK
SSPEEYGHYGKQLLVGNGHNRWFDKSFNLCVGSNGRVGLLNEHTYGDGSVAAHFFEECLI
DDYHCYDKEGKLKVKVENKSSLPKPEKLEWSLIDIDLIDAVEKAHEDVMNVVNNVDHQIK
LHKSFGRGFMKKCKVSPDAFIQMAVQLAYYRQHQKFSLTYEPAMTRLFKKGRTETIRSCT
IESSTWAKSMDNKNSIKEEKLKLFKKACEKHQQMYLDAMFGNGVDRHLFALQTAAKLNGS
ESNFLNEACNEPFMMLTSHIPHAQSPKSNHDNVKDFFITAGAAMPPGIHKGYSISYFPFD
DELLFFHVSSMKNCNSTDTTKLLNGIFQALTDIKNLFVENEK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g14114.t1 Gene3D G3DSA:3.30.559.40 - 103 693 3.5E-180
8 g14114.t1 Gene3D G3DSA:3.30.559.70 - 162 478 3.5E-180
2 g14114.t1 PANTHER PTHR22589:SF31 CARNITINE PALMITOYLTRANSFERASE I 32 699 1.2E-220
3 g14114.t1 PANTHER PTHR22589 CARNITINE O-ACYLTRANSFERASE 32 699 1.2E-220
1 g14114.t1 Pfam PF00755 Choline/Carnitine o-acyltransferase 103 694 2.5E-173
11 g14114.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 11 -
14 g14114.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 31 -
10 g14114.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 32 37 -
13 g14114.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 38 60 -
12 g14114.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 61 702 -
7 g14114.t1 SUPERFAMILY SSF52777 CoA-dependent acyltransferases 95 469 4.73E-106
6 g14114.t1 SUPERFAMILY SSF52777 CoA-dependent acyltransferases 475 697 6.67E-62
4 g14114.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 10 24 -
5 g14114.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 37 59 -

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.

Raw TPM values