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 g5138 g5138.t2 isoform g5138.t2 7241429 7242057
chr_2 g5138 g5138.t2 exon g5138.t2.exon1 7241429 7241850
chr_2 g5138 g5138.t2 cds g5138.t2.CDS1 7241429 7241850
chr_2 g5138 g5138.t2 exon g5138.t2.exon2 7241922 7242057
chr_2 g5138 g5138.t2 cds g5138.t2.CDS2 7241922 7242057
chr_2 g5138 g5138.t2 TSS g5138.t2 7242871 7242871
chr_2 g5138 g5138.t2 TTS g5138.t2 NA NA

Sequences

>g5138.t2 Gene=g5138 Length=558
ATGGTGAGAGGTTGCTGGTGGTATTACTTCAGTAAATTCACAGAATTCTTTGATACATTC
TTCTTTGTCTTAAGAAAGCGATATGACCAAGTTTCAACTTTGCACGTCATTCATCATGGA
ATCATGCCTTTTAGTGTTTGGTGGGGAGTAAAATTCATGCCAGGCGGCCACAGCACATTT
TTTGCATTTCTCAACACTTTCGTTCATATTGTGATGTATACTTACTACATGTTAGCAGCA
ATAGGACCAGAAATGCAAAGATATCTCTGGTGGAAGAAATATTTGACAATTTTGCAGATG
GTGCAGTTTGCAGTAGTTTTTATTCACGCCTTTCAATTGCTATTCAGTAATCCATGCAAT
TATCCAATTGCTTTTGTTTATTGGATTCTTGCACACTCTGTTTTGTTTTTATTTTTATTT
GGTGGATTTTATAAGGACACTTATGTTAAAAATAACAAAAGAAAGCAAGCAATTTGTGAC
ATGAATGGAAATGCTGTGAAAAATCATAAAATTTATCAGGAATCAAATAATAATAGTCAA
ATAAAGAAATTTAATTAA

>g5138.t2 Gene=g5138 Length=185
MVRGCWWYYFSKFTEFFDTFFFVLRKRYDQVSTLHVIHHGIMPFSVWWGVKFMPGGHSTF
FAFLNTFVHIVMYTYYMLAAIGPEMQRYLWWKKYLTILQMVQFAVVFIHAFQLLFSNPCN
YPIAFVYWILAHSVLFLFLFGGFYKDTYVKNNKRKQAICDMNGNAVKNHKIYQESNNNSQ
IKKFN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g5138.t2 PANTHER PTHR11157 FATTY ACID ACYL TRANSFERASE-RELATED 1 159 1.0E-88
3 g5138.t2 PANTHER PTHR11157:SF151 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 1 159 1.0E-88
1 g5138.t2 Pfam PF01151 GNS1/SUR4 family 5 155 1.5E-45
12 g5138.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
18 g5138.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 24 -
8 g5138.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 25 30 -
17 g5138.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 31 50 -
13 g5138.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 51 61 -
15 g5138.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 62 82 -
9 g5138.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 83 93 -
16 g5138.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 94 115 -
11 g5138.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 116 120 -
14 g5138.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 121 144 -
10 g5138.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 145 185 -
7 g5138.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 31 50 -
6 g5138.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 60 82 -
4 g5138.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 94 116 -
5 g5138.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 121 143 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5138/g5138.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5138.t2.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. There were no conditions that were differentially expressed