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.t3 isoform g5143.t3 7259942 7261175
chr_2 g5143 g5143.t3 exon g5143.t3.exon1 7259942 7260787
chr_2 g5143 g5143.t3 TTS g5143.t3 7259954 7259954
chr_2 g5143 g5143.t3 cds g5143.t3.CDS1 7260309 7260787
chr_2 g5143 g5143.t3 exon g5143.t3.exon2 7260861 7261175
chr_2 g5143 g5143.t3 cds g5143.t3.CDS2 7260861 7261170
chr_2 g5143 g5143.t3 TSS g5143.t3 NA NA

Sequences

>g5143.t3 Gene=g5143 Length=1161
GATTTATGCAAGACAGAAAACCATTCAAGCTTCGAAAAATTATAATTGTTTATAATTTTT
TGCAAGTGCTATTTAGTTTGTATCTATTTCTCGAAGTAGCAAGCGTTGGATGGATAGGAG
GTGGATATAGCTGGAGATGTCAACCAGTTAATCACTCAACAGATGCAGACACAATGAGAA
TGGTCAGCGTATGCTGGTGGTATTATTTCAGTAAATTCACAGAGTTCTTTGATACATTCT
TCTTCGTCTTAAGAAAACGATATGATCAAGTTTCAACTTTGCACGTTATTCATCATGGAA
TCATGCCATTCAGCGTTTGGTGGGGAGTAAAATTCATGCCAGGTGGTCACAGTTCATTCT
TTGGATTCCTCAACACTTTCGTTCATATTGTTATGTATACTTACTACATGTTAGCAGCAA
TGGGACCAGAAATGCAAAAATATCTCTGGTGGAAAAAGTATTTGACAATGTTCCAAATGA
TTCAATTTATTGGAATTTTCACACATGCATTCCAATTGTTCTTCCACAATCCATGCAACT
ATCCAATTGTGTTGGCTTACTGGATCGGCGGTCATGGCGTTTTGTTCTTGTTCCTCTTTG
CAAATTTCTATAAGCAAGCTTATACAAAGAAGGAAGTCAAGGTAAAAGTTGATCGAGATA
TCAACGAAAATGCACTGAACGGAGGCAATGGACTTTATGAAGCAAAACAGAAAGCAGCAA
CTGCATTTGATCAAAATGGAAATCATGCATACAGTAATGGAGTGCGAAATAGAATCACTG
CAGTGGCGGAATAATATTTCTTGTTGGGCAAAGCCATCCCTTTCTTACAAGTCACGTCGT
TTTCATTTAAACCCTTGGTGCTGATTGGGTTTAATTTTGAATTTTACTTCTTTATTTTTA
ATGTTTAAAAACAGCCACACAACAATACACAGATTTTTTTAAGATTGTACTTAATGACAA
AAAAAACTATATAAAATAAGTGATAAATGTATAACTAGGAGTTAATTAGAATGAGATGCT
GCAATGAACATGATGATTAAGGAAAGTTTTATGATCTAAATACAAATTTTTATACATACT
GAGAAGAGAAAAAAGAAAGAAATGTAAAAAAACTATTTAATAAAGACAACTTAAACTTAA
TTTATAGCTAAAATAATATAT

>g5143.t3 Gene=g5143 Length=262
MQDRKPFKLRKIIIVYNFLQVLFSLYLFLEVASVGWIGGGYSWRCQPVNHSTDADTMRMV
SVCWWYYFSKFTEFFDTFFFVLRKRYDQVSTLHVIHHGIMPFSVWWGVKFMPGGHSSFFG
FLNTFVHIVMYTYYMLAAMGPEMQKYLWWKKYLTMFQMIQFIGIFTHAFQLFFHNPCNYP
IVLAYWIGGHGVLFLFLFANFYKQAYTKKEVKVKVDRDINENALNGGNGLYEAKQKAATA
FDQNGNHAYSNGVRNRITAVAE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g5143.t3 Coils Coil Coil 260 262 -
2 g5143.t3 PANTHER PTHR11157 FATTY ACID ACYL TRANSFERASE-RELATED 1 224 6.5E-116
3 g5143.t3 PANTHER PTHR11157:SF151 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 1 224 6.5E-116
1 g5143.t3 Pfam PF01151 GNS1/SUR4 family 1 212 1.9E-58
12 g5143.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
19 g5143.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 29 -
17 g5143.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 30 63 -
22 g5143.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 64 82 -
11 g5143.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 83 88 -
23 g5143.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 89 108 -
15 g5143.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 109 119 -
21 g5143.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 120 140 -
14 g5143.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 141 151 -
18 g5143.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 152 173 -
16 g5143.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 174 178 -
20 g5143.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 179 202 -
13 g5143.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 203 262 -
7 g5143.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 12 34 -
6 g5143.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 60 82 -
9 g5143.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 89 108 -
8 g5143.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 118 140 -
5 g5143.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 152 174 -
4 g5143.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 179 201 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5143/g5143.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5143.t3.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