Gene loci information

Transcript annotation

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

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_2 g5143 g5143.t6 TTS g5143.t6 7259954 7259954
chr_2 g5143 g5143.t6 isoform g5143.t6 7260309 7261015
chr_2 g5143 g5143.t6 exon g5143.t6.exon1 7260309 7260775
chr_2 g5143 g5143.t6 cds g5143.t6.CDS1 7260309 7260775
chr_2 g5143 g5143.t6 exon g5143.t6.exon2 7260861 7261015
chr_2 g5143 g5143.t6 cds g5143.t6.CDS2 7260861 7261002
chr_2 g5143 g5143.t6 TSS g5143.t6 NA NA

Sequences

>g5143.t6 Gene=g5143 Length=622
AGATGCAGACACAATGAGAATGGTCAGCGTATGCTGGTGGTATTATTTCAGTAAATTCAC
AGAGTTCTTTGATACATTCTTCTTCGTCTTAAGAAAACGATATGATCAAGTTTCAACTTT
GCACGTTATTCATCATGGAATCATGCCATTCAGCGTAAAATTCATGCCAGGTGGTCACAG
TTCATTCTTTGGATTCCTCAACACTTTCGTTCATATTGTTATGTATACTTACTACATGTT
AGCAGCAATGGGACCAGAAATGCAAAAATATCTCTGGTGGAAAAAGTATTTGACAATGTT
CCAAATGATTCAATTTATTGGAATTTTCACACATGCATTCCAATTGTTCTTCCACAATCC
ATGCAACTATCCAATTGTGTTGGCTTACTGGATCGGCGGTCATGGCGTTTTGTTCTTGTT
CCTCTTTGCAAATTTCTATAAGCAAGCTTATACAAAGAAGGAAGTCAAGGTAAAAGTTGA
TCGAGATATCAACGAAAATGCACTGAACGGAGGCAATGGACTTTATGAAGCAAAACAGAA
AGCAGCAACTGCATTTGATCAAAATGGAAATCATGCATACAGTAATGGAGTGCGAAATAG
AATCACTGCAGTGGCGGAATAA

>g5143.t6 Gene=g5143 Length=202
MRMVSVCWWYYFSKFTEFFDTFFFVLRKRYDQVSTLHVIHHGIMPFSVKFMPGGHSSFFG
FLNTFVHIVMYTYYMLAAMGPEMQKYLWWKKYLTMFQMIQFIGIFTHAFQLFFHNPCNYP
IVLAYWIGGHGVLFLFLFANFYKQAYTKKEVKVKVDRDINENALNGGNGLYEAKQKAATA
FDQNGNHAYSNGVRNRITAVAE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g5143.t6 PANTHER PTHR11157 FATTY ACID ACYL TRANSFERASE-RELATED 1 165 4.8E-85
3 g5143.t6 PANTHER PTHR11157:SF151 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 1 165 4.8E-85
1 g5143.t6 Pfam PF01151 GNS1/SUR4 family 4 152 1.0E-39
11 g5143.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 57 -
14 g5143.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 58 80 -
9 g5143.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 81 91 -
13 g5143.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 92 113 -
10 g5143.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 114 118 -
12 g5143.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 119 142 -
8 g5143.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 143 202 -
6 g5143.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 7 26 -
7 g5143.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 58 80 -
4 g5143.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 92 114 -
5 g5143.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 119 141 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5143/g5143.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5143.t6.fa.iupred3.txt does not exist

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.

Raw TPM values