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_1 g12190 g12190.t5 TTS g12190.t5 21658510 21658510
chr_1 g12190 g12190.t5 isoform g12190.t5 21658682 21659594
chr_1 g12190 g12190.t5 exon g12190.t5.exon1 21658682 21659145
chr_1 g12190 g12190.t5 cds g12190.t5.CDS1 21658682 21659145
chr_1 g12190 g12190.t5 exon g12190.t5.exon2 21659328 21659460
chr_1 g12190 g12190.t5 cds g12190.t5.CDS2 21659328 21659460
chr_1 g12190 g12190.t5 exon g12190.t5.exon3 21659571 21659594
chr_1 g12190 g12190.t5 TSS g12190.t5 21659757 21659757

Sequences

>g12190.t5 Gene=g12190 Length=621
TCTTATAGTGCACAAGCCATACAGATGACACACTTTTGTTGGTGGTATTACTTCAGTAAA
TTTACAGAGTTCTTTGACACATTTTTCTTTGTTTTGAGAAAAAGATATGATCAAGTTTCA
ACTTTGCATGTAATTCATCATGGAATTATGCCTTTTATATGGTGGGGAGTGAAATTCATG
CCTGGCGGTCACAGCACCTTCTTTGGACTCCTCAACACATTTGTGCATATCATAATGTAT
ACTTATTATATGTTAGCTGCAATGGGACCACAAGTTCAAAAATATCTTTGGTGGAAAAAA
TATCTAACAATTTTGCAGATGATCCAATTTGTTGGAATTTTTACTCATTGCTTCCAACTG
ATCTTCCATAATCCCTGCAATTACTCTTATATTTTTGTATATTGGATTGGTGGTCATGGT
GTGCTGTTTTATTTCCTCTTTAGAAGCTTCTATCAACAAGCTTATGTGGCGAAATCAAAA
TCAGTAAAAAATGATGAACCAAATGACAAAAAGACATTAATTGTAGATGACAATGAAAAT
ATTGTAGAATACAAGAAACATTATGAGACAAAAAGAGACTCAATAACACAGATTAATAAG
GCACTAGCGAAGCATCTTTAA

>g12190.t5 Gene=g12190 Length=198
MTHFCWWYYFSKFTEFFDTFFFVLRKRYDQVSTLHVIHHGIMPFIWWGVKFMPGGHSTFF
GLLNTFVHIIMYTYYMLAAMGPQVQKYLWWKKYLTILQMIQFVGIFTHCFQLIFHNPCNY
SYIFVYWIGGHGVLFYFLFRSFYQQAYVAKSKSVKNDEPNDKKTLIVDDNENIVEYKKHY
ETKRDSITQINKALAKHL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g12190.t5 PANTHER PTHR11157 FATTY ACID ACYL TRANSFERASE-RELATED 2 170 2.2E-85
3 g12190.t5 PANTHER PTHR11157:SF151 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 2 170 2.2E-85
1 g12190.t5 Pfam PF01151 GNS1/SUR4 family 3 153 1.7E-40
11 g12190.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
18 g12190.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 24 -
9 g12190.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 25 30 -
16 g12190.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 31 49 -
13 g12190.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 50 60 -
17 g12190.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 61 81 -
8 g12190.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 82 92 -
14 g12190.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 93 114 -
12 g12190.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 115 119 -
15 g12190.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 120 139 -
10 g12190.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 140 198 -
7 g12190.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 31 49 -
6 g12190.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 59 81 -
4 g12190.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 93 115 -
5 g12190.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 120 142 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

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