Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Elongation of very long chain fatty acids protein F.

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 g13609 g13609.t2 isoform g13609.t2 31280576 31281712
chr_1 g13609 g13609.t2 exon g13609.t2.exon1 31280576 31280703
chr_1 g13609 g13609.t2 cds g13609.t2.CDS1 31280697 31280703
chr_1 g13609 g13609.t2 exon g13609.t2.exon2 31280845 31281119
chr_1 g13609 g13609.t2 cds g13609.t2.CDS2 31280845 31281119
chr_1 g13609 g13609.t2 exon g13609.t2.exon3 31281184 31281324
chr_1 g13609 g13609.t2 cds g13609.t2.CDS3 31281184 31281324
chr_1 g13609 g13609.t2 exon g13609.t2.exon4 31281384 31281712
chr_1 g13609 g13609.t2 cds g13609.t2.CDS4 31281384 31281548
chr_1 g13609 g13609.t2 TSS g13609.t2 NA NA
chr_1 g13609 g13609.t2 TTS g13609.t2 NA NA

Sequences

>g13609.t2 Gene=g13609 Length=873
ATGGTGTCTTTGGGTTATATATCTGAAATTTGGAATAAATATGAAGGTAGAAATGAAGTT
TTTTTTATTTGAATTTATTTACCGAACTGAAAATTATTTGAAAACTAATTACATAAAAAT
GAATAAAAAATTTTTTAGATCCTAGAACAGCAGGAAAATTTCTTATGGAAAATCCACCTA
CGAGATTTTTCGGATTTATAATTTCATATGTATTGTTCATTCACTTTGGACCAACTTTAA
TGAAGAAAAGAAAACCGTTTGAATTAAAATTAGTGAAATCTGTTTACAACATTTTTCAAA
TTGTCATAAATGGATATTACGGACTTTATGGACTGTATTATGTATTTTTAACACATAATT
ACAATTATTCTTGCCCATCATTGGCTATTGGAAATGATGAATATGCTCAGACAATTGCAC
ACTTGGGACATATTTATTTCTTATCAAAACTTTGGGATCTTTTTGATACTATTTTCATAA
TATTAAAAAAGAATGATCGACAGTTATCATTTCTTCATTGCTATCATCATTTGTTTATGG
CTTTTGCAACTTATTTTATTATGAAATTTTACATTGATACATCTTTCTGTTTGGTTGCTG
TCATCAATGCTTTGATTCATAGCTGCATGTATTTTTACTATTTTCTCACAACGCAAAATT
CGGAAGTTAAGAAATCAATCACATGGAAGAAACATATTACACATATTCAAATGGTAAGTG
TTGTGGAAATAATTTCTTTTGACACAATGTAATAGACCGAAAGTTTGGGATATATTTATG
TCTCTTCAGATTCTTTTTATCCTTTATATGTTCATACAATTCTATATTAAAACATATTTA
GTAAAGAAGAATTCAAATAAAAAGAAATTTTAA

>g13609.t2 Gene=g13609 Length=195
MENPPTRFFGFIISYVLFIHFGPTLMKKRKPFELKLVKSVYNIFQIVINGYYGLYGLYYV
FLTHNYNYSCPSLAIGNDEYAQTIAHLGHIYFLSKLWDLFDTIFIILKKNDRQLSFLHCY
HHLFMAFATYFIMKFYIDTSFCLVAVINALIHSCMYFYYFLTTQNSEVKKSITWKKHITH
IQMVSVVEIISFDTM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g13609.t2 PANTHER PTHR11157 FATTY ACID ACYL TRANSFERASE-RELATED 10 190 6.5E-48
3 g13609.t2 PANTHER PTHR11157:SF116 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN-RELATED 10 190 6.5E-48
1 g13609.t2 Pfam PF01151 GNS1/SUR4 family 5 187 2.8E-41
13 g13609.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
16 g13609.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 25 -
9 g13609.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 26 45 -
18 g13609.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 46 64 -
12 g13609.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 65 83 -
15 g13609.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 84 107 -
8 g13609.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 108 118 -
17 g13609.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 119 137 -
11 g13609.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 138 142 -
14 g13609.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 143 161 -
10 g13609.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 162 195 -
7 g13609.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 7 26 -
6 g13609.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 41 63 -
4 g13609.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 114 133 -
5 g13609.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 143 162 -

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:0016021 integral component of membrane CC

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

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