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.t4 isoform g5143.t4 7259942 7268384
chr_2 g5143 g5143.t4 exon g5143.t4.exon1 7259942 7260787
chr_2 g5143 g5143.t4 TTS g5143.t4 7259954 7259954
chr_2 g5143 g5143.t4 cds g5143.t4.CDS1 7260309 7260787
chr_2 g5143 g5143.t4 exon g5143.t4.exon2 7260861 7261188
chr_2 g5143 g5143.t4 cds g5143.t4.CDS2 7260861 7261188
chr_2 g5143 g5143.t4 exon g5143.t4.exon3 7266583 7266723
chr_2 g5143 g5143.t4 cds g5143.t4.CDS3 7266583 7266681
chr_2 g5143 g5143.t4 exon g5143.t4.exon4 7268368 7268384
chr_2 g5143 g5143.t4 TSS g5143.t4 7268645 7268645

Sequences

>g5143.t4 Gene=g5143 Length=1332
AAAATATTAAGTTAAAGATGAACATAATCAACAAATTCTACCATGAATGGAGGGATCTGA
TGGATAACAAATCTGATCAGAGAACGACAAATTGGATGCTAATGTCATCGCCAATTCCAA
CAGTCATCATTTGCTTGTCTTATGTTTATATTGTCAAGGTACTTGGACCACGATTTATGC
AAGACAGAAAACCATTCAAGCTTCGAAAAATTATAATTGTTTATAATTTTTTGCAAGTGC
TATTTAGTTTGTATCTATTTCTCGAAGTAGCAAGCGTTGGATGGATAGGAGGTGGATATA
GCTGGAGATGTCAACCAGTTAATCACTCAACAGATGCAGACACAATGAGAATGGTCAGCG
TATGCTGGTGGTATTATTTCAGTAAATTCACAGAGTTCTTTGATACATTCTTCTTCGTCT
TAAGAAAACGATATGATCAAGTTTCAACTTTGCACGTTATTCATCATGGAATCATGCCAT
TCAGCGTTTGGTGGGGAGTAAAATTCATGCCAGGTGGTCACAGTTCATTCTTTGGATTCC
TCAACACTTTCGTTCATATTGTTATGTATACTTACTACATGTTAGCAGCAATGGGACCAG
AAATGCAAAAATATCTCTGGTGGAAAAAGTATTTGACAATGTTCCAAATGATTCAATTTA
TTGGAATTTTCACACATGCATTCCAATTGTTCTTCCACAATCCATGCAACTATCCAATTG
TGTTGGCTTACTGGATCGGCGGTCATGGCGTTTTGTTCTTGTTCCTCTTTGCAAATTTCT
ATAAGCAAGCTTATACAAAGAAGGAAGTCAAGGTAAAAGTTGATCGAGATATCAACGAAA
ATGCACTGAACGGAGGCAATGGACTTTATGAAGCAAAACAGAAAGCAGCAACTGCATTTG
ATCAAAATGGAAATCATGCATACAGTAATGGAGTGCGAAATAGAATCACTGCAGTGGCGG
AATAATATTTCTTGTTGGGCAAAGCCATCCCTTTCTTACAAGTCACGTCGTTTTCATTTA
AACCCTTGGTGCTGATTGGGTTTAATTTTGAATTTTACTTCTTTATTTTTAATGTTTAAA
AACAGCCACACAACAATACACAGATTTTTTTAAGATTGTACTTAATGACAAAAAAAACTA
TATAAAATAAGTGATAAATGTATAACTAGGAGTTAATTAGAATGAGATGCTGCAATGAAC
ATGATGATTAAGGAAAGTTTTATGATCTAAATACAAATTTTTATACATACTGAGAAGAGA
AAAAAGAAAGAAATGTAAAAAAACTATTTAATAAAGACAACTTAAACTTAATTTATAGCT
AAAATAATATAT

>g5143.t4 Gene=g5143 Length=301
MDNKSDQRTTNWMLMSSPIPTVIICLSYVYIVKVLGPRFMQDRKPFKLRKIIIVYNFLQV
LFSLYLFLEVASVGWIGGGYSWRCQPVNHSTDADTMRMVSVCWWYYFSKFTEFFDTFFFV
LRKRYDQVSTLHVIHHGIMPFSVWWGVKFMPGGHSSFFGFLNTFVHIVMYTYYMLAAMGP
EMQKYLWWKKYLTMFQMIQFIGIFTHAFQLFFHNPCNYPIVLAYWIGGHGVLFLFLFANF
YKQAYTKKEVKVKVDRDINENALNGGNGLYEAKQKAATAFDQNGNHAYSNGVRNRITAVA
E

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g5143.t4 PANTHER PTHR11157 FATTY ACID ACYL TRANSFERASE-RELATED 1 263 2.9E-138
3 g5143.t4 PANTHER PTHR11157:SF151 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 1 263 2.9E-138
1 g5143.t4 Pfam PF01151 GNS1/SUR4 family 14 251 2.4E-64
17 g5143.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 11 -
24 g5143.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 31 -
11 g5143.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 32 51 -
20 g5143.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 52 76 -
18 g5143.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 77 102 -
23 g5143.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 103 121 -
14 g5143.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 122 127 -
21 g5143.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 128 147 -
16 g5143.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 148 158 -
19 g5143.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 159 179 -
13 g5143.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 180 190 -
25 g5143.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 191 212 -
15 g5143.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 213 217 -
22 g5143.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 218 241 -
12 g5143.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 242 301 -
10 g5143.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 10 32 -
6 g5143.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 53 75 -
9 g5143.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 99 121 -
8 g5143.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 128 147 -
4 g5143.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 157 179 -
7 g5143.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 191 213 -
5 g5143.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 218 240 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5143/g5143.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5143.t4.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0016021 integral component of membrane CC

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

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