Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Carnitine O-palmitoyltransferase 1, muscle 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 g14120 g14120.t6 TSS g14120.t6 34803623 34803623
chr_1 g14120 g14120.t6 isoform g14120.t6 34803624 34806839
chr_1 g14120 g14120.t6 exon g14120.t6.exon1 34803624 34803805
chr_1 g14120 g14120.t6 exon g14120.t6.exon2 34806017 34806383
chr_1 g14120 g14120.t6 cds g14120.t6.CDS1 34806106 34806383
chr_1 g14120 g14120.t6 exon g14120.t6.exon3 34806454 34806638
chr_1 g14120 g14120.t6 cds g14120.t6.CDS2 34806454 34806638
chr_1 g14120 g14120.t6 exon g14120.t6.exon4 34806710 34806839
chr_1 g14120 g14120.t6 cds g14120.t6.CDS3 34806710 34806837
chr_1 g14120 g14120.t6 TTS g14120.t6 NA NA

Sequences

>g14120.t6 Gene=g14120 Length=864
AGTTTCATTCGAAGCATGTGCCAGTGATCGTGTAATTTTCATTACGCTCCTCTTGATAAA
GACAATTTTTATTTTCAATACAAAATAATTTCTAGTGAGAATTTTTAGTTATTTTCACAA
CAATAAGTAAATTAGTGATATTTTCTGCAATAAAATTTTTAAGTGTGCAATTGCATTTCA
AGATACTGCTTTTATTTCAATCATAAAGTTTAGCATCGGATAAAAATATAAAATTTTTAA
GAGGAAAGGCTAAACCTCTTATGAGTTAATTATGGCTGAAGCCCATCAAGCCGTTGCCTT
TAGTTTTGCTATCACTCATGAAGGATTTAATGTCAACTATGATCGTGAAGTTCTTCATCT
TGTCTGGGAATCAGGTGTGAGATCATGGAAGAAAAGAGTCGCAAGAATAAAAGCTGGAAT
TAAAAATGGAGCTTATCCAGCTCATTTAGAATCACTTTATGTTATTATGATATTAGTAAC
ATTACTACATTTCTCAAACAAAACAGTTCCATATGATTTGGTCAATACATTTATGAATGT
AATGCCAAGTAATGGATCATTTTGGCACTTTCTCTCATGTGTTCTTGTATCACTTTTTTA
TTGGATTTTGATTTGTTTAATTATGCGTTATTCATTGAAAGGATTATTGGTCTATAAAGG
CTGGATGTATGAAGCACGTGGATCAGGTTCTAAACCAAGTCTTAAAACAAAAATTTGGTT
TGTCCTTGTTAAAGTCTTTAAAAAATGGAATAGCCCGGGATTATACAGTTTTCAATCATC
ACTTCCTCGTTTACCACTTCCGAGTGTGAATGACACAATGACAAGATGGTTGAGATCTGT
TCGACCACTTGTTGATGATGCGAC

>g14120.t6 Gene=g14120 Length=197
MAEAHQAVAFSFAITHEGFNVNYDREVLHLVWESGVRSWKKRVARIKAGIKNGAYPAHLE
SLYVIMILVTLLHFSNKTVPYDLVNTFMNVMPSNGSFWHFLSCVLVSLFYWILICLIMRY
SLKGLLVYKGWMYEARGSGSKPSLKTKIWFVLVKVFKKWNSPGLYSFQSSLPRLPLPSVN
DTMTRWLRSVRPLVDDA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g14120.t6 Gene3D G3DSA:1.10.275.20 - 154 197 1.2E-8
2 g14120.t6 PANTHER PTHR22589:SF31 CARNITINE PALMITOYLTRANSFERASE I 55 196 7.6E-27
3 g14120.t6 PANTHER PTHR22589 CARNITINE O-ACYLTRANSFERASE 55 196 7.6E-27
1 g14120.t6 Pfam PF16484 Carnitine O-palmitoyltransferase N-terminus 1 47 9.9E-25
9 g14120.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 54 -
12 g14120.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 55 76 -
10 g14120.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 77 95 -
11 g14120.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 96 122 -
8 g14120.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 123 197 -
6 g14120.t6 SUPERFAMILY SSF52777 CoA-dependent acyltransferases 164 196 1.11E-8
5 g14120.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 53 75 -
4 g14120.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 95 117 -

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