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.t18 TTS g12190.t18 21658510 21658510
chr_1 g12190 g12190.t18 isoform g12190.t18 21659344 21664727
chr_1 g12190 g12190.t18 exon g12190.t18.exon1 21659344 21659460
chr_1 g12190 g12190.t18 cds g12190.t18.CDS1 21659344 21659460
chr_1 g12190 g12190.t18 exon g12190.t18.exon2 21659571 21659759
chr_1 g12190 g12190.t18 cds g12190.t18.CDS2 21659571 21659759
chr_1 g12190 g12190.t18 exon g12190.t18.exon3 21661922 21662062
chr_1 g12190 g12190.t18 cds g12190.t18.CDS3 21661922 21662062
chr_1 g12190 g12190.t18 exon g12190.t18.exon4 21664628 21664727
chr_1 g12190 g12190.t18 cds g12190.t18.CDS4 21664628 21664630
chr_1 g12190 g12190.t18 TSS g12190.t18 21664861 21664861

Sequences

>g12190.t18 Gene=g12190 Length=547
TATTTAAACAACTGCAAGAAAATAAATTTAGAAGTGAAATAAAAATAGTGAAATTATTTT
TAAATTATAACATTCAGAAAGAATTAATAAAAAATAGATGATGGATGCTCTAAACAAAAT
TAGTGCCACATGGCAAGACTTAATGGACAACAAGTCCGATCCAAGAACGACAAATTGGTT
CCTTATGTCATCGCCACTTCCCACTGTGATGATCTGCCTTACATATGTTTATTTAGTCAA
GATAGTTGGTCCTGCGCTTATGGAAAATCGAAAGCCATTTCAGTTAAGAAAAATCATTGT
AGTTTATAATTTTCTGCAAGTACTACTGAGTGCTTGGCTGTTTTGGGGTTTGGGAAAATC
GGGATGGTTCACAAATTATAGTTACAGATGTCAACCAGTAGATTTATCTTATAGTGCACA
AGCCATACAGATGACACACTTTTGTTGGTGGTATTACTTCAGTAAATTTACAGAGTTCTT
TGACACATTTTTCTTTGTTTTGAGAAAAAGATATGATCAAGTTTCAACTTTGCATGTAAT
TCATCAT

>g12190.t18 Gene=g12190 Length=150
MMDALNKISATWQDLMDNKSDPRTTNWFLMSSPLPTVMICLTYVYLVKIVGPALMENRKP
FQLRKIIVVYNFLQVLLSAWLFWGLGKSGWFTNYSYRCQPVDLSYSAQAIQMTHFCWWYY
FSKFTEFFDTFFFVLRKRYDQVSTLHVIHH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g12190.t18 PANTHER PTHR11157 FATTY ACID ACYL TRANSFERASE-RELATED 5 150 6.7E-72
3 g12190.t18 PANTHER PTHR11157:SF151 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 5 150 6.7E-72
1 g12190.t18 Pfam PF01151 GNS1/SUR4 family 29 150 4.0E-29
9 g12190.t18 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 26 -
13 g12190.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 27 46 -
7 g12190.t18 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 47 66 -
12 g12190.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 67 86 -
10 g12190.t18 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 87 116 -
11 g12190.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 117 135 -
8 g12190.t18 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 136 150 -
6 g12190.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 25 47 -
5 g12190.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 67 86 -
4 g12190.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 113 135 -

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