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_3 g4160 g4160.t2 isoform g4160.t2 31059263 31060117
chr_3 g4160 g4160.t2 exon g4160.t2.exon1 31059263 31059454
chr_3 g4160 g4160.t2 cds g4160.t2.CDS1 31059362 31059454
chr_3 g4160 g4160.t2 exon g4160.t2.exon2 31059509 31059652
chr_3 g4160 g4160.t2 cds g4160.t2.CDS2 31059509 31059652
chr_3 g4160 g4160.t2 exon g4160.t2.exon3 31059713 31060117
chr_3 g4160 g4160.t2 cds g4160.t2.CDS3 31059713 31060117
chr_3 g4160 g4160.t2 TTS g4160.t2 31060149 31060149
chr_3 g4160 g4160.t2 TSS g4160.t2 NA NA

Sequences

>g4160.t2 Gene=g4160 Length=741
GATGAAAGAATCAAGGATCTCTTTTTAATAAATTCACCTTGGCCTTTGGTCATAATTGTT
ACTGCATATCTCTATTTTGTCAATGGAAATGGTCAAAAAATGATGAAATATCGAGAGCCT
TTTGAATTAAATGGAATAATAAATATTTATAACATCATACAAGTATTCTTGAATCTTTAT
TTAGCTATTGGGGCAACATGGACATTAATCGGAATTAAAGATTTGAATATTCTATGTATT
CCAGAAGCAAGAAAAATGATTTCGGATGAAGGAAAGAAAATAGTGTATTTTTCTCATCTC
TATTATTTGATTAAAGTTGTAGATTTACTCGATACGATCTTTTTTATCTTAAGAAAGAAA
AACAATCAAGTATCATTTTTGCATATTTATCATCATACGATTATGGTTGTTGGTTGCTAC
ATATACATTAAATTTATGGTCGGCGGAGGACAACCAACCTCTCTCGGAATAATAAATTCT
TTCGTTCATGTCGTCATGTATTCATATTATTTTCTAACATCATTTAAACCTGAGCTTAAG
AAATCAATATGGTGGAAAAAGCATATAACTCAACTTCAAATGACGCAGTTTGCAATTCTA
GTGATTCATTTCCTCATGCCAGTGTTTACCGAATGTGATTACCCTAAAGGGTTATCTGCA
GGAATCGCCTTTCAAAATATATTTATGTTTTTACTTTTTGCTGATTTTTATTATAAAGCT
TATGTAAAAACTAAAAAGTAA

>g4160.t2 Gene=g4160 Length=213
MMKYREPFELNGIINIYNIIQVFLNLYLAIGATWTLIGIKDLNILCIPEARKMISDEGKK
IVYFSHLYYLIKVVDLLDTIFFILRKKNNQVSFLHIYHHTIMVVGCYIYIKFMVGGGQPT
SLGIINSFVHVVMYSYYFLTSFKPELKKSIWWKKHITQLQMTQFAILVIHFLMPVFTECD
YPKGLSAGIAFQNIFMFLLFADFYYKAYVKTKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g4160.t2 PANTHER PTHR11157 FATTY ACID ACYL TRANSFERASE-RELATED 1 210 4.5E-72
3 g4160.t2 PANTHER PTHR11157:SF21 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 1 210 4.5E-72
1 g4160.t2 Pfam PF01151 GNS1/SUR4 family 1 213 5.1E-50
10 g4160.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
18 g4160.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 37 -
14 g4160.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 38 60 -
20 g4160.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 61 84 -
12 g4160.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 85 95 -
22 g4160.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 96 114 -
15 g4160.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 115 119 -
21 g4160.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 120 139 -
11 g4160.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 140 158 -
17 g4160.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 159 177 -
16 g4160.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 178 188 -
19 g4160.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 189 205 -
13 g4160.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 206 213 -
5 g4160.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 35 -
6 g4160.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 62 84 -
4 g4160.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 91 110 -
7 g4160.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 120 142 -
9 g4160.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 155 177 -
8 g4160.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 187 209 -

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

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