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.t5 TTS g5143.t5 7259954 7259954
chr_2 g5143 g5143.t5 isoform g5143.t5 7260109 7268647
chr_2 g5143 g5143.t5 exon g5143.t5.exon1 7260109 7260273
chr_2 g5143 g5143.t5 cds g5143.t5.CDS1 7260253 7260273
chr_2 g5143 g5143.t5 exon g5143.t5.exon2 7260342 7260787
chr_2 g5143 g5143.t5 cds g5143.t5.CDS2 7260342 7260787
chr_2 g5143 g5143.t5 exon g5143.t5.exon3 7260966 7261188
chr_2 g5143 g5143.t5 cds g5143.t5.CDS3 7260966 7261188
chr_2 g5143 g5143.t5 exon g5143.t5.exon4 7266583 7266723
chr_2 g5143 g5143.t5 cds g5143.t5.CDS4 7266583 7266681
chr_2 g5143 g5143.t5 exon g5143.t5.exon5 7268368 7268647
chr_2 g5143 g5143.t5 TSS g5143.t5 7268645 7268645

Sequences

>g5143.t5 Gene=g5143 Length=1255
GTCAGTCTACGGTCAGCTCTCACGGCATTCGGATCGCGAGGAATTTTTCTCCTCTAAAAT
TCAGAGCAAATTGACTCTTATATTATTTGTGCTTTTTTGGTATTATAAGAAAAAAGACTT
ATAAAATTTTTTTTTGCAAATCAACAAACAGAAAAAAAGAAATCATAAGAGAGACAAAAT
AGAAACAAAAGTGACCAGTTTTTTTCTTAATTTTAAATTTAGTGAAATAACAAAAATTTT
AAGTCAAAGAAACAAAAAACAATAAAATATTAAGTTAAAGATGAACATAATCAACAAATT
CTACCATGAATGGAGGGATCTGATGGATAACAAATCTGATCAGAGAACGACAAATTGGAT
GCTAATGTCATCGCCAATTCCAACAGTCATCATTTGCTTGTCTTATGTTTATATTGTCAA
GGTACTTGGACCACGATTTATGCAAGACAGAAAACCATTCAAGCTTCGAAAAATTATAAT
TGTTTATAATTTTTTGCAAGTGCTATTTAGTTTGTATCTATTTCTCGAAGTAGCAAGCGT
TGGATGGATAGGAGGTGGATATAGCTGGAGATGTCAACCAGTTAATCACTCAACAGATGC
AGACACAATGAGAATGGTCAGCGTATGCTGGTGGTATTATTTCATTTGGTGGGGAGTAAA
ATTCATGCCAGGTGGTCACAGTTCATTCTTTGGATTCCTCAACACTTTCGTTCATATTGT
TATGTATACTTACTACATGTTAGCAGCAATGGGACCAGAAATGCAAAAATATCTCTGGTG
GAAAAAGTATTTGACAATGTTCCAAATGATTCAATTTATTGGAATTTTCACACATGCATT
CCAATTGTTCTTCCACAATCCATGCAACTATCCAATTGTGTTGGCTTACTGGATCGGCGG
TCATGGCGTTTTGTTCTTGTTCCTCTTTGCAAATTTCTATAAGCAAGCTTATACAAAGAA
GGAAGTCAAGGTAAAAGTTGATCGAGATATCAACGAAAATGCACTGAACGGAGGCAATGG
ACTTTATGAAGCAAAACAGAAAGCAGCAACTGCATTTGATCAAAATGGAAATCATGCATA
CAGTAATGGAAGTCACGTCGTTTTCATTTAAACCCTTGGTGCTGATTGGGTTTAATTTTG
AATTTTACTTCTTTATTTTTAATGTTTAAAAACAGCCACACAACAATACACAGATTTTTT
TAAGATTGTACTTAATGACAAAAAAAACTATATAAAATAAGTGATAAATGTATAA

>g5143.t5 Gene=g5143 Length=262
MDNKSDQRTTNWMLMSSPIPTVIICLSYVYIVKVLGPRFMQDRKPFKLRKIIIVYNFLQV
LFSLYLFLEVASVGWIGGGYSWRCQPVNHSTDADTMRMVSVCWWYYFIWWGVKFMPGGHS
SFFGFLNTFVHIVMYTYYMLAAMGPEMQKYLWWKKYLTMFQMIQFIGIFTHAFQLFFHNP
CNYPIVLAYWIGGHGVLFLFLFANFYKQAYTKKEVKVKVDRDINENALNGGNGLYEAKQK
AATAFDQNGNHAYSNGSHVVFI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
3 g5143.t5 PANTHER PTHR11157 FATTY ACID ACYL TRANSFERASE-RELATED 1 107 4.4E-104
5 g5143.t5 PANTHER PTHR11157:SF151 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 1 107 4.4E-104
4 g5143.t5 PANTHER PTHR11157 FATTY ACID ACYL TRANSFERASE-RELATED 108 227 4.4E-104
6 g5143.t5 PANTHER PTHR11157:SF151 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 108 227 4.4E-104
2 g5143.t5 Pfam PF01151 GNS1/SUR4 family 14 107 1.7E-16
1 g5143.t5 Pfam PF01151 GNS1/SUR4 family 107 216 8.9E-26
16 g5143.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 11 -
22 g5143.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 31 -
14 g5143.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 32 51 -
20 g5143.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 52 76 -
15 g5143.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 77 121 -
19 g5143.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 122 144 -
12 g5143.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 145 155 -
21 g5143.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 156 177 -
17 g5143.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 178 182 -
18 g5143.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 183 206 -
13 g5143.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 207 262 -
11 g5143.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 10 32 -
10 g5143.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 53 75 -
9 g5143.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 122 144 -
7 g5143.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 156 178 -
8 g5143.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 183 205 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5143/g5143.t5; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5143.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