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.t13 TTS g12190.t13 21658510 21658510
chr_1 g12190 g12190.t13 isoform g12190.t13 21658682 21664887
chr_1 g12190 g12190.t13 exon g12190.t13.exon1 21658682 21659145
chr_1 g12190 g12190.t13 cds g12190.t13.CDS1 21658682 21659145
chr_1 g12190 g12190.t13 exon g12190.t13.exon2 21659325 21659460
chr_1 g12190 g12190.t13 cds g12190.t13.CDS2 21659325 21659460
chr_1 g12190 g12190.t13 exon g12190.t13.exon3 21659571 21659755
chr_1 g12190 g12190.t13 cds g12190.t13.CDS3 21659571 21659741
chr_1 g12190 g12190.t13 exon g12190.t13.exon4 21661922 21662062
chr_1 g12190 g12190.t13 exon g12190.t13.exon5 21664628 21664887
chr_1 g12190 g12190.t13 TSS g12190.t13 21664861 21664861

Sequences

>g12190.t13 Gene=g12190 Length=1186
GTGAGTGTTAAATTATTCGGATTTTCAGTCTTTCATTAGCGTTTAAATCGCACGCATCAT
TCTCCAGTTTTATTAAAAGTGAAGAAGTGAAATAGACACTTGAAAAATATTTTTATAAAT
ATTATTTATGTGATGAATTTACTTTAATAAAAAGAATAATTATTTAAACAACTGCAAGAA
AATAAATTTAGAAGTGAAATAAAAATAGTGAAATTATTTTTAAATTATAACATTCAGAAA
GAATTAATAAAAAATAGATGATGGATGCTCTAAACAAAATTAGTGCCACATGGCAAGACT
TAATGGACAACAAGTCCGATCCAAGAACGACAAATTGGTTCCTTATGTCATCGCCACTTC
CCACTGTGATGATCTGCCTTACATATGTTTATTTAGTCAAGTTGGTCCTGCGCTTATGGA
AAATCGAAAGCCATTTCAGTTAAGAAAAATCATTGTAGTTTATAATTTTCTGCAAGTACT
ACTGAGTGCTTGGCTGTTTTGGGGTTTGGGAAAATCGGGATGGTTCACAAATTATAGTTA
CAGATGTCAACCAGTAGATTTATCTTATAGTGCACAAGCCATACAGATGACACACTTTTG
TTGGTGGTATTACTTCAGTAAATTTACAGAGTTCTTTGACACATTTTTCTTTGTTTTGAG
AAAAAGATATGATCAAGTTTCAACTTTGCATGTAATTCATCATGGAATTATGCCTTTTAG
TGTATGGTGGGGAGTGAAATTCATGCCTGGCGGTCACAGCACCTTCTTTGGACTCCTCAA
CACATTTGTGCATATCATAATGTATACTTATTATATGTTAGCTGCAATGGGACCACAAGT
TCAAAAATATCTTTGGTGGAAAAAATATCTAACAATTTTGCAGATGATCCAATTTGTTGG
AATTTTTACTCATTGCTTCCAACTGATCTTCCATAATCCCTGCAATTACTCTTATATTTT
TGTATATTGGATTGGTGGTCATGGTGTGCTGTTTTATTTCCTCTTTAGAAGCTTCTATCA
ACAAGCTTATGTGGCGAAATCAAAATCAGTAAAAAATGATGAACCAAATGACAAAAAGAC
ATTAATTGTAGATGACAATGAAAATATTGTAGAATACAAGAAACATTATGAGACAAAAAG
AGACTCAATAACACAGATTAATAAGGCACTAGCGAAGCATCTTTAA

>g12190.t13 Gene=g12190 Length=256
MENRKPFQLRKIIVVYNFLQVLLSAWLFWGLGKSGWFTNYSYRCQPVDLSYSAQAIQMTH
FCWWYYFSKFTEFFDTFFFVLRKRYDQVSTLHVIHHGIMPFSVWWGVKFMPGGHSTFFGL
LNTFVHIIMYTYYMLAAMGPQVQKYLWWKKYLTILQMIQFVGIFTHCFQLIFHNPCNYSY
IFVYWIGGHGVLFYFLFRSFYQQAYVAKSKSVKNDEPNDKKTLIVDDNENIVEYKKHYET
KRDSITQINKALAKHL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g12190.t13 PANTHER PTHR11157 FATTY ACID ACYL TRANSFERASE-RELATED 1 228 9.9E-117
3 g12190.t13 PANTHER PTHR11157:SF151 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 1 228 9.9E-117
1 g12190.t13 Pfam PF01151 GNS1/SUR4 family 1 211 7.3E-54
10 g12190.t13 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
18 g12190.t13 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 29 -
16 g12190.t13 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 30 48 -
22 g12190.t13 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 49 67 -
11 g12190.t13 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 68 87 -
17 g12190.t13 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 88 107 -
14 g12190.t13 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 108 118 -
19 g12190.t13 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 119 139 -
13 g12190.t13 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 140 150 -
21 g12190.t13 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 151 172 -
15 g12190.t13 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 173 177 -
20 g12190.t13 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 178 197 -
12 g12190.t13 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 198 256 -
9 g12190.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 32 -
7 g12190.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 59 81 -
4 g12190.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 88 107 -
6 g12190.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 117 139 -
5 g12190.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 151 173 -
8 g12190.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 178 200 -

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