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.t5 TTS g5142.t5 7252080 7252080
chr_2 g5142 g5142.t5 isoform g5142.t5 7252084 7253658
chr_2 g5142 g5142.t5 exon g5142.t5.exon1 7252084 7252859
chr_2 g5142 g5142.t5 cds g5142.t5.CDS1 7252456 7252859
chr_2 g5142 g5142.t5 exon g5142.t5.exon2 7252928 7253063
chr_2 g5142 g5142.t5 cds g5142.t5.CDS2 7252928 7253063
chr_2 g5142 g5142.t5 exon g5142.t5.exon3 7253131 7253658
chr_2 g5142 g5142.t5 cds g5142.t5.CDS3 7253131 7253241
chr_2 g5142 g5142.t5 TSS g5142.t5 NA NA

Sequences

>g5142.t5 Gene=g5142 Length=1440
ATGGATATTATCACTCGTATACATGCCGGATGGAGAGATCTAATGGATAACAAAACAGAC
CCGCGAGTCGCTAAATGGCCATTGGCAGCATCTCCGTTTCCCACATTGTTTATCTGCTTA
GCTTATGTTTACATTGTCAAGGTAAAGATTATTATAATTTCAATTGACATTCAACTACGT
TATTCATTAGCTTGTGATTTGATTTTGATATTTTTTCAATGGACTTTAAGTGAAAATCAA
ATTAAAAATAACTACTTGTTTATTACGACACTTGATTTTGTTAATTTGATAACAAGTTTG
CGAATTTCAACTAACGTAATGTTTTTTTGATTTCAGGTTCTTGGACCACGATTTATGCAA
GACAGAAAGCCATTTAATCTTCGGAAAGTGATAATTTTTTATAACTTTTTGCAAGTCATG
CTGAGTTTCTATCTATTTTGGGAAGTGTCCGTTGTTGGATGGATAGGAGGTGGTTACAAT
TGGCGCTGTCAACCTGTCGACTTTTCTCGCAATGAAATGCCAATGAGAATGGCAAGAGTT
TGTTGGCTATATTTTATTAGTAAATTCACAGAATTTTTCGACACATTCTTCTTTGTTTTG
AGAAAAAGATACGACCAAGTTTCAACACTTCATATCATTCATCACAGAATTATGCCATTT
AGTGTTTGGTGGGGTTTAAAGTTTATGCCTGGAGGTCATAGCACGTTTTTTTTCTTTCTT
AATACATTCGTTCATATTGTGATGTATACTTACTACATGTTAGCAGCAATGGGACCAGAA
ATGCAAAAATATCTCTGGTGGAAACGATATTTGACAATGTTCCAAATGATTCAATTTATT
GGAATTTTCACACATGCATTCCAATTGTTCTTCCACAATCCATGCAACTATCCGATTGTT
TTCTCTTACTGGATTGGTGGTCATGGTGTTTTGTTCTTGTTCCTTTTCGCTAATTTCTAT
GTACAAACTTATACAAAGAAAAAGAGCAAGAAAACTTTAGAAAATGGAAAAGTTAATGGT
TTAATTAAGAAAGAAATTGAAACAAATGGATTGAAAAAGGAACTGTAAAATGAATTTATT
AATTAGTATTTGCCATTTGAGGAGTTCTAAGTTTTCTTATTTGAAAAAGCTTAATGATTA
TTTTAAGATGTTAGTCAGAAATTAGAAAATTAAGATAAATATTGATTAAAGGAACAAAAA
TCGACTGAAGAGAACTGCTTTTAAAGAGCAGCACCAAAGGTCATTTTTTAATTAATTAAA
CTCTGGCGATTTGGTTCCATTTAAAGGATAATTTTAGCATTTTTTACTTTGATGAACTTT
ATAAAATTTAATACGCATGACAAGTGATATAATTGCTAAATAAATTTTTATTAAACAGCA
CTTTTAATAAATAGAAATTGGTGTGAAATATTTATTGCTAATAAAAATTATTTTTTATCA

>g5142.t5 Gene=g5142 Length=216
MLSFYLFWEVSVVGWIGGGYNWRCQPVDFSRNEMPMRMARVCWLYFISKFTEFFDTFFFV
LRKRYDQVSTLHIIHHRIMPFSVWWGLKFMPGGHSTFFFFLNTFVHIVMYTYYMLAAMGP
EMQKYLWWKRYLTMFQMIQFIGIFTHAFQLFFHNPCNYPIVFSYWIGGHGVLFLFLFANF
YVQTYTKKKSKKTLENGKVNGLIKKEIETNGLKKEL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g5142.t5 PANTHER PTHR11157 FATTY ACID ACYL TRANSFERASE-RELATED 2 196 9.7E-97
3 g5142.t5 PANTHER PTHR11157:SF151 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 2 196 9.7E-97
1 g5142.t5 Pfam PF01151 GNS1/SUR4 family 2 192 1.6E-49
13 g5142.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
19 g5142.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 22 -
10 g5142.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 23 42 -
15 g5142.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 43 61 -
14 g5142.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 62 96 -
16 g5142.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 97 119 -
9 g5142.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 120 130 -
18 g5142.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 131 152 -
12 g5142.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 153 163 -
17 g5142.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 164 182 -
11 g5142.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 183 216 -
8 g5142.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 5 22 -
7 g5142.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 42 61 -
4 g5142.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 97 119 -
6 g5142.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 131 150 -
5 g5142.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 160 182 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5142/g5142.t5; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5142.t5.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