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 g14115 g14115.t15 isoform g14115.t15 34787965 34789540
chr_1 g14115 g14115.t15 exon g14115.t15.exon1 34787965 34788708
chr_1 g14115 g14115.t15 cds g14115.t15.CDS1 34787967 34788708
chr_1 g14115 g14115.t15 exon g14115.t15.exon2 34788797 34789081
chr_1 g14115 g14115.t15 cds g14115.t15.CDS2 34788797 34789065
chr_1 g14115 g14115.t15 exon g14115.t15.exon3 34789517 34789540
chr_1 g14115 g14115.t15 TSS g14115.t15 34789544 34789544
chr_1 g14115 g14115.t15 TTS g14115.t15 NA NA

Sequences

>g14115.t15 Gene=g14115 Length=1053
AGTGCACAGCGCCTGAGCAGAGAGAAATTAAAAGAGAAAAATGTCTGGTTTTCGTGCATC
TTCTACTACTGAAATTAAAGATTATATCGATGCGCATCACAATGACGAAATTCTTCAGTT
AGTTTGGTTGTCCGGTTTAAAGTCCTGGAAACATCGCTACGCAGTATTTAAGCGCAAAGT
CCAGAATGGTGTTTACCCCGCTCATTTAGAGTCTCTTTTCGTCATCATTGTCGTTGTTAT
GGCATTTCATTTTTCGTCTACAAAAGTTCCATATGACTTACTTAATACCTTCATTTCACT
TTTACCGAGTAATTTGATCGACTGGCAGATACTGTTATGTGTTATCATTGGATTTTTATG
GTGGTTGTCGATATGTTTGACATTACGTTATACATTAAAATTATTGCTAATGTACAAGGG
ATATTTATTTGAAACTCGAGGAAAAGGAGTTAGTTTAAAGACAAAAGTGTGGGCAATTTT
AGTTAAACTTTTGCTCAAATGGAATTCCCCGGTATTGTACAGTTTTCAAGGATCTCTACC
TCGTTTGTCTGTTCCTGATGTTAACGATACAATTAAACGCTACCTCGCTTCAGTTCGTCC
AATTTATGACGATGAAACTTATGATAAAGTGTGTAAAGATGCTGAATTTTTTGAAAACGG
AATTGCAAAGAAGTTGCAACGGTATTTGGTGTTGAAGAGTTGGTGGGCAGATAACTATGT
ATCAGATTGGTGGGAAGAGTATGCTTATCTAAAAAGCCGTGAACCGTTGATGTATGGTAG
TAATTATTACGGTAGTGATACTATTTATCCACCAACAAATAGTCAAGCTGCACGAGCTGC
TAATCTCGCTTATCTCATGCTTAAATTTCGAGATAAAATTGTTCATCAAGAATTGCCACC
AATTATGCTACAATCAATGGTTCCTCTTTGCTCATCTCAATATGAAAGACTTTTCAATAC
AGCTCGAATTCCAGGAATTGAAAGTGATAAAATTATTCACGTTGAAGATTCAAAGCACAT
TGTGGTGATGCATAAAGGATCTTATTATAAACT

>g14115.t15 Gene=g14115 Length=337
MSGFRASSTTEIKDYIDAHHNDEILQLVWLSGLKSWKHRYAVFKRKVQNGVYPAHLESLF
VIIVVVMAFHFSSTKVPYDLLNTFISLLPSNLIDWQILLCVIIGFLWWLSICLTLRYTLK
LLLMYKGYLFETRGKGVSLKTKVWAILVKLLLKWNSPVLYSFQGSLPRLSVPDVNDTIKR
YLASVRPIYDDETYDKVCKDAEFFENGIAKKLQRYLVLKSWWADNYVSDWWEEYAYLKSR
EPLMYGSNYYGSDTIYPPTNSQAARAANLAYLMLKFRDKIVHQELPPIMLQSMVPLCSSQ
YERLFNTARIPGIESDKIIHVEDSKHIVVMHKGSYYK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g14115.t15 Gene3D G3DSA:3.30.559.40 - 166 224 1.7E-56
7 g14115.t15 Gene3D G3DSA:3.30.559.70 - 225 337 1.7E-56
2 g14115.t15 PANTHER PTHR22589:SF31 CARNITINE PALMITOYLTRANSFERASE I 55 337 5.0E-91
3 g14115.t15 PANTHER PTHR22589 CARNITINE O-ACYLTRANSFERASE 55 337 5.0E-91
1 g14115.t15 Pfam PF00755 Choline/Carnitine o-acyltransferase 166 337 1.1E-55
10 g14115.t15 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 53 -
13 g14115.t15 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 54 73 -
11 g14115.t15 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 74 92 -
12 g14115.t15 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 93 115 -
9 g14115.t15 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 116 337 -
6 g14115.t15 SUPERFAMILY SSF52777 CoA-dependent acyltransferases 158 337 3.39E-61
5 g14115.t15 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 51 73 -
4 g14115.t15 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 93 115 -

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