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.t11 TTS g12190.t11 21658510 21658510
chr_1 g12190 g12190.t11 isoform g12190.t11 21658682 21664879
chr_1 g12190 g12190.t11 exon g12190.t11.exon1 21658682 21659145
chr_1 g12190 g12190.t11 cds g12190.t11.CDS1 21658682 21659145
chr_1 g12190 g12190.t11 exon g12190.t11.exon2 21659325 21659460
chr_1 g12190 g12190.t11 cds g12190.t11.CDS2 21659325 21659460
chr_1 g12190 g12190.t11 exon g12190.t11.exon3 21659571 21659759
chr_1 g12190 g12190.t11 cds g12190.t11.CDS3 21659571 21659759
chr_1 g12190 g12190.t11 exon g12190.t11.exon4 21661922 21661987
chr_1 g12190 g12190.t11 cds g12190.t11.CDS4 21661922 21661978
chr_1 g12190 g12190.t11 exon g12190.t11.exon5 21664727 21664879
chr_1 g12190 g12190.t11 TSS g12190.t11 21664861 21664861

Sequences

>g12190.t11 Gene=g12190 Length=1008
TAAATTATTCGGATTTTCAGTCTTTCATTAGCGTTTAAATCGCACGCATCATTCTCCAGT
TTTATTAAAAGTGAAGAAGTGAAATAGACACTTGAAAAATATTTTTATAAATATTATTTA
TGTGATGAATTTACTTTAATAAAAAGAATAATTTGGTTCCTTATGTCATCGCCACTTCCC
ACTGTGATGATCTGCCTTACATATGTTTATTTAGTCAAGATAGTTGGTCCTGCGCTTATG
GAAAATCGAAAGCCATTTCAGTTAAGAAAAATCATTGTAGTTTATAATTTTCTGCAAGTA
CTACTGAGTGCTTGGCTGTTTTGGGGTTTGGGAAAATCGGGATGGTTCACAAATTATAGT
TACAGATGTCAACCAGTAGATTTATCTTATAGTGCACAAGCCATACAGATGACACACTTT
TGTTGGTGGTATTACTTCAGTAAATTTACAGAGTTCTTTGACACATTTTTCTTTGTTTTG
AGAAAAAGATATGATCAAGTTTCAACTTTGCATGTAATTCATCATGGAATTATGCCTTTT
AGTGTATGGTGGGGAGTGAAATTCATGCCTGGCGGTCACAGCACCTTCTTTGGACTCCTC
AACACATTTGTGCATATCATAATGTATACTTATTATATGTTAGCTGCAATGGGACCACAA
GTTCAAAAATATCTTTGGTGGAAAAAATATCTAACAATTTTGCAGATGATCCAATTTGTT
GGAATTTTTACTCATTGCTTCCAACTGATCTTCCATAATCCCTGCAATTACTCTTATATT
TTTGTATATTGGATTGGTGGTCATGGTGTGCTGTTTTATTTCCTCTTTAGAAGCTTCTAT
CAACAAGCTTATGTGGCGAAATCAAAATCAGTAAAAAATGATGAACCAAATGACAAAAAG
ACATTAATTGTAGATGACAATGAAAATATTGTAGAATACAAGAAACATTATGAGACAAAA
AGAGACTCAATAACACAGATTAATAAGGCACTAGCGAAGCATCTTTAA

>g12190.t11 Gene=g12190 Length=281
MSSPLPTVMICLTYVYLVKIVGPALMENRKPFQLRKIIVVYNFLQVLLSAWLFWGLGKSG
WFTNYSYRCQPVDLSYSAQAIQMTHFCWWYYFSKFTEFFDTFFFVLRKRYDQVSTLHVIH
HGIMPFSVWWGVKFMPGGHSTFFGLLNTFVHIIMYTYYMLAAMGPQVQKYLWWKKYLTIL
QMIQFVGIFTHCFQLIFHNPCNYSYIFVYWIGGHGVLFYFLFRSFYQQAYVAKSKSVKND
EPNDKKTLIVDDNENIVEYKKHYETKRDSITQINKALAKHL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g12190.t11 PANTHER PTHR11157 FATTY ACID ACYL TRANSFERASE-RELATED 1 253 3.6E-131
3 g12190.t11 PANTHER PTHR11157:SF151 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 1 253 3.6E-131
1 g12190.t11 Pfam PF01151 GNS1/SUR4 family 1 236 3.2E-59
17 g12190.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
20 g12190.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 25 -
11 g12190.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 26 36 -
21 g12190.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 37 54 -
16 g12190.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 55 73 -
19 g12190.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 74 92 -
14 g12190.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 93 112 -
23 g12190.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 113 132 -
18 g12190.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 133 143 -
25 g12190.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 144 164 -
13 g12190.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 165 175 -
22 g12190.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 176 197 -
15 g12190.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 198 202 -
24 g12190.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 203 222 -
12 g12190.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 223 281 -
4 g12190.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 4 26 -
8 g12190.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 38 57 -
7 g12190.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 84 106 -
6 g12190.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 113 132 -
5 g12190.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 142 164 -
9 g12190.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 176 198 -
10 g12190.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 203 225 -

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