Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t6 isoform g14115.t6 34786514 34789065
chr_1 g14115 g14115.t6 exon g14115.t6.exon1 34786514 34786808
chr_1 g14115 g14115.t6 cds g14115.t6.CDS1 34786514 34786808
chr_1 g14115 g14115.t6 exon g14115.t6.exon2 34788851 34789065
chr_1 g14115 g14115.t6 cds g14115.t6.CDS2 34788851 34789065
chr_1 g14115 g14115.t6 TSS g14115.t6 34789544 34789544
chr_1 g14115 g14115.t6 TTS g14115.t6 NA NA

Sequences

>g14115.t6 Gene=g14115 Length=510
ATGTCTGGTTTTCGTGCATCTTCTACTACTGAAATTAAAGATTATATCGATGCGCATCAC
AATGACGAAATTCTTCAGTTAGTTTGGTTGTCCGGTTTAAAGTCCTGGAAACATCGCTAC
GCAGTATTTAAGCGCAAAGTCCAGAATGGTGTTTACCCCGCTCATTTAGAGTCTCTTTTC
GTCATCATTGTCGTTGTTATGGCATTTCATTTTTCATTTTTGGATAAAGTATTTAGTGAA
CCATGGCGTTTAACTACATCACAGACACCATTAGGTCAAACACCTAAAACAGACATAAAT
AAATTTAAACAACTTTATACAGCCAGTGGTGGATTTGGACCTGTCGTTTCAGATGGTTAT
GGAGTTTCATATATAATTTTGAGAGATGATATAATTTTCTTTCATGTATCCAGTAAAAAA
AGCTGCTCAGTTACTAACACAGACAGATTCGGAAAACAAATTGTCAAAGCAATGTCTGAC
ATCAAACAGTTATTTGAACTTGCAAATTAA

>g14115.t6 Gene=g14115 Length=169
MSGFRASSTTEIKDYIDAHHNDEILQLVWLSGLKSWKHRYAVFKRKVQNGVYPAHLESLF
VIIVVVMAFHFSFLDKVFSEPWRLTTSQTPLGQTPKTDINKFKQLYTASGGFGPVVSDGY
GVSYIILRDDIIFFHVSSKKSCSVTNTDRFGKQIVKAMSDIKQLFELAN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g14115.t6 Gene3D G3DSA:3.30.559.40 - 52 169 4.4E-24
2 g14115.t6 PANTHER PTHR22589:SF31 CARNITINE PALMITOYLTRANSFERASE I 12 166 1.1E-31
3 g14115.t6 PANTHER PTHR22589 CARNITINE O-ACYLTRANSFERASE 12 166 1.1E-31
1 g14115.t6 Pfam PF00755 Choline/Carnitine o-acyltransferase 73 162 6.6E-17
9 g14115.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 53 -
10 g14115.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 54 74 -
8 g14115.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 75 169 -
6 g14115.t6 SUPERFAMILY SSF52777 CoA-dependent acyltransferases 9 166 3.39E-19
5 g14115.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 51 73 -
4 g14115.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 105 127 -

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