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 g5142 g5142.t11 TTS g5142.t11 7252080 7252080
chr_2 g5142 g5142.t11 isoform g5142.t11 7252456 7256378
chr_2 g5142 g5142.t11 exon g5142.t11.exon1 7252456 7252859
chr_2 g5142 g5142.t11 cds g5142.t11.CDS1 7252456 7252859
chr_2 g5142 g5142.t11 exon g5142.t11.exon2 7252928 7253063
chr_2 g5142 g5142.t11 cds g5142.t11.CDS2 7252928 7253063
chr_2 g5142 g5142.t11 exon g5142.t11.exon3 7253131 7253322
chr_2 g5142 g5142.t11 cds g5142.t11.CDS3 7253131 7253322
chr_2 g5142 g5142.t11 exon g5142.t11.exon4 7253533 7253658
chr_2 g5142 g5142.t11 cds g5142.t11.CDS4 7253533 7253658
chr_2 g5142 g5142.t11 exon g5142.t11.exon5 7256267 7256378
chr_2 g5142 g5142.t11 TSS g5142.t11 7256375 7256375

Sequences

>g5142.t11 Gene=g5142 Length=970
CTCAGTCGCGTTTCAACTTTTAAACTCATCAGTTGTGCAAAAAAAGAAATTTCGTCAATA
AATTTTAATTTTTAGTTTTTAAATCAGTGAAAGAAAAGGAAAGTTTTAAAAAATGGATAT
TATCACTCGTATACATGCCGGATGGAGAGATCTAATGGATAACAAAACAGACCCGCGAGT
CGCTAAATGGCCATTGGCAGCATCTCCGTTTCCCACATTGTTTATCTGCTTAGCTTATGT
TCTTGGACCACGATTTATGCAAGACAGAAAGCCATTTAATCTTCGGAAAGTGATAATTTT
TTATAACTTTTTGCAAGTCATGCTGAGTTTCTATCTATTTTGGGAAGTGTCCGTTGTTGG
ATGGATAGGAGGTGGTTACAATTGGCGCTGTCAACCTGTCGACTTTTCTCGCAATGAAAT
GCCAATGAGAATGGCAAGAGTTTGTTGGCTATATTTTATTAGTAAATTCACAGAATTTTT
CGACACATTCTTCTTTGTTTTGAGAAAAAGATACGACCAAGTTTCAACACTTCATATCAT
TCATCACAGAATTATGCCATTTAGTGTTTGGTGGGGTTTAAAGTTTATGCCTGGAGGTCA
TAGCACGTTTTTTTTCTTTCTTAATACATTCGTTCATATTGTGATGTATACTTACTACAT
GTTAGCAGCAATGGGACCAGAAATGCAAAAATATCTCTGGTGGAAACGATATTTGACAAT
GTTCCAAATGATTCAATTTATTGGAATTTTCACACATGCATTCCAATTGTTCTTCCACAA
TCCATGCAACTATCCGATTGTTTTCTCTTACTGGATTGGTGGTCATGGTGTTTTGTTCTT
GTTCCTTTTCGCTAATTTCTATGTACAAACTTATACAAAGAAAAAGAGCAAGAAAACTTT
AGAAAATGGAAAAGTTAATGGTTTAATTAAGAAAGAAATTGAAACAAATGGATTGAAAAA
GGAACTGTAA

>g5142.t11 Gene=g5142 Length=285
MDIITRIHAGWRDLMDNKTDPRVAKWPLAASPFPTLFICLAYVLGPRFMQDRKPFNLRKV
IIFYNFLQVMLSFYLFWEVSVVGWIGGGYNWRCQPVDFSRNEMPMRMARVCWLYFISKFT
EFFDTFFFVLRKRYDQVSTLHIIHHRIMPFSVWWGLKFMPGGHSTFFFFLNTFVHIVMYT
YYMLAAMGPEMQKYLWWKRYLTMFQMIQFIGIFTHAFQLFFHNPCNYPIVFSYWIGGHGV
LFLFLFANFYVQTYTKKKSKKTLENGKVNGLIKKEIETNGLKKEL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g5142.t11 PANTHER PTHR11157 FATTY ACID ACYL TRANSFERASE-RELATED 3 264 1.1E-130
3 g5142.t11 PANTHER PTHR11157:SF151 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 3 264 1.1E-130
1 g5142.t11 Pfam PF01151 GNS1/SUR4 family 29 261 4.5E-61
17 g5142.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 25 -
19 g5142.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 26 45 -
11 g5142.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 46 56 -
24 g5142.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 57 77 -
16 g5142.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 78 111 -
23 g5142.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 112 130 -
10 g5142.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 131 136 -
22 g5142.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 137 156 -
15 g5142.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 157 167 -
21 g5142.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 168 188 -
12 g5142.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 189 199 -
18 g5142.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 200 221 -
14 g5142.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 222 232 -
20 g5142.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 233 251 -
13 g5142.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 252 285 -
5 g5142.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 23 45 -
8 g5142.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 60 82 -
4 g5142.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 110 129 -
9 g5142.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 166 188 -
7 g5142.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 200 219 -
6 g5142.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 229 251 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5142/g5142.t11; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5142.t11.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