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 g5140 g5140.t2 TTS g5140.t2 7246308 7246308
chr_2 g5140 g5140.t2 isoform g5140.t2 7246495 7247573
chr_2 g5140 g5140.t2 exon g5140.t2.exon1 7246495 7246886
chr_2 g5140 g5140.t2 cds g5140.t2.CDS1 7246495 7246886
chr_2 g5140 g5140.t2 exon g5140.t2.exon2 7246959 7247091
chr_2 g5140 g5140.t2 cds g5140.t2.CDS2 7246959 7247091
chr_2 g5140 g5140.t2 exon g5140.t2.exon3 7247250 7247573
chr_2 g5140 g5140.t2 cds g5140.t2.CDS3 7247250 7247573
chr_2 g5140 g5140.t2 TSS g5140.t2 7247736 7247736

Sequences

>g5140.t2 Gene=g5140 Length=849
ATGCTTCACAAAATTCAAGCAATTTGGCAAGATTTAATGCAAAATAAATCTGATCCAAGA
GTGGCAAATTTTTTTTTAATGTCATCGCCTTTTCCGACAATAATAATTTGCCTTACTTAT
GTTTATCTCGTGAAAGTTCTATTGCCAAAATTTATGGAAAATCGAAAACCTTTCAAACTA
CAGAAGATATTGATAGTTTACAATTTTGCCCAAGCTTTATTCAGTTTATATTTATTTTCT
GAGGCAGGTCGATATGGGTGGTTCAGGCACTACAGCTGGCGATGCCAAGCAGTTGATTAC
TCACATAACAAACTTGCTATGAAAATGGTCATTGGCAGTTACCTCTATTATTTGAGTAAA
TTTTCTGAATTCTTTGACACTTTCTTTTTTGTTTTGAGAAAGAAATATGATCAAGTTTCA
ACTTTACACGTCATTCATCATGGAATTATGCCTTTTATTTGGTGGGGAGCGAAATTTTTA
CCAGGTGGTCACAGCTCATTCTTTGCTTTTCTCAATACTTTCATTCATTTCGTTATGTAC
ACTTACTACATGTTAGCAGCAATGGGACCAAAAGTGCAGAAATATCTCTGGTGGAAAAAA
TATTTGACTTTGATGCAAATGGCTCAATTTGTGGCAATTTTTGTTCATGCATTTCAACTG
TTCTTTCACAATCCTTGCAATTATCCAATTATTTTTGCTTATTGGATCGGCGGTCATGGA
GTTTTGTTCTTAGTTCTTTTTATGAACTTTTATAAACAAGCATATTTAAAGAAGGATAAA
AAAATCAAAGCAGTTGATTTGAATGAAAATTCTGAATATATTTCAATTGAAGGAAAGAAA
ATTAAGTAA

>g5140.t2 Gene=g5140 Length=282
MLHKIQAIWQDLMQNKSDPRVANFFLMSSPFPTIIICLTYVYLVKVLLPKFMENRKPFKL
QKILIVYNFAQALFSLYLFSEAGRYGWFRHYSWRCQAVDYSHNKLAMKMVIGSYLYYLSK
FSEFFDTFFFVLRKKYDQVSTLHVIHHGIMPFIWWGAKFLPGGHSSFFAFLNTFIHFVMY
TYYMLAAMGPKVQKYLWWKKYLTLMQMAQFVAIFVHAFQLFFHNPCNYPIIFAYWIGGHG
VLFLVLFMNFYKQAYLKKDKKIKAVDLNENSEYISIEGKKIK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g5140.t2 PANTHER PTHR11157 FATTY ACID ACYL TRANSFERASE-RELATED 3 268 9.4E-129
3 g5140.t2 PANTHER PTHR11157:SF151 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 3 268 9.4E-129
1 g5140.t2 Pfam PF01151 GNS1/SUR4 family 26 261 4.5E-60
14 g5140.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 20 -
22 g5140.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 21 43 -
13 g5140.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 44 62 -
24 g5140.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 63 80 -
15 g5140.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 81 113 -
21 g5140.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 114 132 -
11 g5140.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 133 138 -
20 g5140.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 139 157 -
17 g5140.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 158 168 -
23 g5140.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 169 189 -
12 g5140.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 190 200 -
18 g5140.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 201 222 -
16 g5140.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 223 227 -
19 g5140.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 228 251 -
10 g5140.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 252 282 -
8 g5140.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 21 43 -
9 g5140.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 63 80 -
6 g5140.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 110 132 -
4 g5140.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 167 189 -
7 g5140.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 201 223 -
5 g5140.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 228 250 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5140/g5140.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5140.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