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.t15 TTS g12190.t15 21658510 21658510
chr_1 g12190 g12190.t15 isoform g12190.t15 21658682 21665041
chr_1 g12190 g12190.t15 exon g12190.t15.exon1 21658682 21658875
chr_1 g12190 g12190.t15 cds g12190.t15.CDS1 21658860 21658875
chr_1 g12190 g12190.t15 exon g12190.t15.exon2 21659052 21659145
chr_1 g12190 g12190.t15 cds g12190.t15.CDS2 21659052 21659145
chr_1 g12190 g12190.t15 exon g12190.t15.exon3 21659325 21659460
chr_1 g12190 g12190.t15 cds g12190.t15.CDS3 21659325 21659460
chr_1 g12190 g12190.t15 exon g12190.t15.exon4 21659571 21659759
chr_1 g12190 g12190.t15 cds g12190.t15.CDS4 21659571 21659759
chr_1 g12190 g12190.t15 exon g12190.t15.exon5 21661922 21662062
chr_1 g12190 g12190.t15 cds g12190.t15.CDS5 21661922 21662062
chr_1 g12190 g12190.t15 exon g12190.t15.exon6 21664628 21665041
chr_1 g12190 g12190.t15 cds g12190.t15.CDS6 21664628 21664630
chr_1 g12190 g12190.t15 TSS g12190.t15 NA NA

Sequences

>g12190.t15 Gene=g12190 Length=1168
TGTTAAAGAAATCGTCGAAAAGAACTCGCGTATACTTATGCACGTGCTTCGTAACTATAA
AGTTTAATAATTTTTTTTTTTGCTAAACAAGTGACGTAATTTTCGTTAATGACTTTCAAA
ATATCTTAGCAATGCAAAGAGTAATGAAAAAAATGTGAGTGTTAAATTATTCGGATTTTC
AGTCTTTCATTAGCGTTTAAATCGCACGCATCATTCTCCAGTTTTATTAAAAGTGAAGAA
GTGAAATAGACACTTGAAAAATATTTTTATAAATATTATTTATGTGATGAATTTACTTTA
ATAAAAAGAATAATTATTTAAACAACTGCAAGAAAATAAATTTAGAAGTGAAATAAAAAT
AGTGAAATTATTTTTAAATTATAACATTCAGAAAGAATTAATAAAAAATAGATGATGGAT
GCTCTAAACAAAATTAGTGCCACATGGCAAGACTTAATGGACAACAAGTCCGATCCAAGA
ACGACAAATTGGTTCCTTATGTCATCGCCACTTCCCACTGTGATGATCTGCCTTACATAT
GTTTATTTAGTCAAGATAGTTGGTCCTGCGCTTATGGAAAATCGAAAGCCATTTCAGTTA
AGAAAAATCATTGTAGTTTATAATTTTCTGCAAGTACTACTGAGTGCTTGGCTGTTTTGG
GGTTTGGGAAAATCGGGATGGTTCACAAATTATAGTTACAGATGTCAACCAGTAGATTTA
TCTTATAGTGCACAAGCCATACAGATGACACACTTTTGTTGGTGGTATTACTTCAGTAAA
TTTACAGAGTTCTTTGACACATTTTTCTTTGTTTTGAGAAAAAGATATGATCAAGTTTCA
ACTTTGCATGTAATTCATCATGGAATTATGCCTTTTAGTGTATGGTGGGGAGTGAAATTC
ATGCCTGGCGGTCACAGCACCTTCTTTGGACTCCTCAACACATTTGTGCATATCATAATG
TATACTTATTATATTTTATTTCCTCTTTAGAAGCTTCTATCAACAAGCTTATGTGGCGAA
ATCAAAATCAGTAAAAAATGATGAACCAAATGACAAAAAGACATTAATTGTAGATGACAA
TGAAAATATTGTAGAATACAAGAAACATTATGAGACAAAAAGAGACTCAATAACACAGAT
TAATAAGGCACTAGCGAAGCATCTTTAA

>g12190.t15 Gene=g12190 Length=192
MMDALNKISATWQDLMDNKSDPRTTNWFLMSSPLPTVMICLTYVYLVKIVGPALMENRKP
FQLRKIIVVYNFLQVLLSAWLFWGLGKSGWFTNYSYRCQPVDLSYSAQAIQMTHFCWWYY
FSKFTEFFDTFFFVLRKRYDQVSTLHVIHHGIMPFSVWWGVKFMPGGHSTFFGLLNTFVH
IIMYTYYILFPL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g12190.t15 PANTHER PTHR11157 FATTY ACID ACYL TRANSFERASE-RELATED 5 189 1.2E-100
3 g12190.t15 PANTHER PTHR11157:SF151 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 5 189 1.2E-100
1 g12190.t15 Pfam PF01151 GNS1/SUR4 family 29 189 1.7E-44
13 g12190.t15 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 26 -
19 g12190.t15 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 27 46 -
11 g12190.t15 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 47 65 -
17 g12190.t15 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 66 83 -
14 g12190.t15 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 84 102 -
18 g12190.t15 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 103 121 -
10 g12190.t15 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 122 141 -
16 g12190.t15 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 142 159 -
12 g12190.t15 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 160 170 -
15 g12190.t15 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 171 190 -
9 g12190.t15 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 191 192 -
8 g12190.t15 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 25 47 -
7 g12190.t15 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 67 86 -
5 g12190.t15 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 113 135 -
6 g12190.t15 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 142 161 -
4 g12190.t15 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 171 190 -

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