Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t4 TTS g12190.t4 21658510 21658510
chr_1 g12190 g12190.t4 isoform g12190.t4 21658682 21659453
chr_1 g12190 g12190.t4 exon g12190.t4.exon1 21658682 21659145
chr_1 g12190 g12190.t4 cds g12190.t4.CDS1 21658682 21659145
chr_1 g12190 g12190.t4 exon g12190.t4.exon2 21659328 21659453
chr_1 g12190 g12190.t4 cds g12190.t4.CDS2 21659328 21659337
chr_1 g12190 g12190.t4 TSS g12190.t4 21659757 21659757

Sequences

>g12190.t4 Gene=g12190 Length=590
ACTTTTGTTGGTGGTATTACTTCAGTAAATTTACAGAGTTCTTTGACACATTTTTCTTTG
TTTTGAGAAAAAGATATGATCAAGTTTCAACTTTGCATGTAATTCATCATGGAATTATGC
CTTTTATATGGTGGGGAGTGAAATTCATGCCTGGCGGTCACAGCACCTTCTTTGGACTCC
TCAACACATTTGTGCATATCATAATGTATACTTATTATATGTTAGCTGCAATGGGACCAC
AAGTTCAAAAATATCTTTGGTGGAAAAAATATCTAACAATTTTGCAGATGATCCAATTTG
TTGGAATTTTTACTCATTGCTTCCAACTGATCTTCCATAATCCCTGCAATTACTCTTATA
TTTTTGTATATTGGATTGGTGGTCATGGTGTGCTGTTTTATTTCCTCTTTAGAAGCTTCT
ATCAACAAGCTTATGTGGCGAAATCAAAATCAGTAAAAAATGATGAACCAAATGACAAAA
AGACATTAATTGTAGATGACAATGAAAATATTGTAGAATACAAGAAACATTATGAGACAA
AAAGAGACTCAATAACACAGATTAATAAGGCACTAGCGAAGCATCTTTAA

>g12190.t4 Gene=g12190 Length=157
MPFIWWGVKFMPGGHSTFFGLLNTFVHIIMYTYYMLAAMGPQVQKYLWWKKYLTILQMIQ
FVGIFTHCFQLIFHNPCNYSYIFVYWIGGHGVLFYFLFRSFYQQAYVAKSKSVKNDEPND
KKTLIVDDNENIVEYKKHYETKRDSITQINKALAKHL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g12190.t4 PANTHER PTHR11157 FATTY ACID ACYL TRANSFERASE-RELATED 4 130 3.7E-58
3 g12190.t4 PANTHER PTHR11157:SF151 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 4 130 3.7E-58
1 g12190.t4 Pfam PF01151 GNS1/SUR4 family 2 112 1.9E-24
9 g12190.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 19 -
12 g12190.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 20 40 -
7 g12190.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 41 51 -
11 g12190.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 52 73 -
10 g12190.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 74 78 -
13 g12190.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 79 98 -
8 g12190.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 99 157 -
5 g12190.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 18 40 -
6 g12190.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 52 74 -
4 g12190.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 79 101 -

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