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.t6 TTS g12190.t6 21658510 21658510
chr_1 g12190 g12190.t6 isoform g12190.t6 21658682 21662585
chr_1 g12190 g12190.t6 exon g12190.t6.exon1 21658682 21659145
chr_1 g12190 g12190.t6 cds g12190.t6.CDS1 21658682 21659145
chr_1 g12190 g12190.t6 exon g12190.t6.exon2 21659325 21659460
chr_1 g12190 g12190.t6 cds g12190.t6.CDS2 21659325 21659460
chr_1 g12190 g12190.t6 exon g12190.t6.exon3 21659571 21659759
chr_1 g12190 g12190.t6 cds g12190.t6.CDS3 21659571 21659759
chr_1 g12190 g12190.t6 exon g12190.t6.exon4 21661922 21662062
chr_1 g12190 g12190.t6 cds g12190.t6.CDS4 21661922 21662062
chr_1 g12190 g12190.t6 exon g12190.t6.exon5 21662312 21662585
chr_1 g12190 g12190.t6 TSS g12190.t6 NA NA

Sequences

>g12190.t6 Gene=g12190 Length=1204
TGTAAGAATTTTATTTGTTCAAAGTGCTCACAATTGTTTTTTTATCGAATAGTAAACCAG
TTATACGTGATTAAGCAATACATAGCATTTCAATCATTTATCGCGCTCATTTCATGTTGA
AAACAGTCAAAACGCGTTGCTAAAAAAAAGTTATTTATCATTTATTCCCTCGCAATTGTC
TCTTGATTCATCCAGTAAATAAATATTGAAATTAAAGAAGACGACCTTCCACAAACGAAC
CTTTATTTGTTCATCGTTTAATGCATACTCTTCGATGGATGCTCTAAACAAAATTAGTGC
CACATGGCAAGACTTAATGGACAACAAGTCCGATCCAAGAACGACAAATTGGTTCCTTAT
GTCATCGCCACTTCCCACTGTGATGATCTGCCTTACATATGTTTATTTAGTCAAGATAGT
TGGTCCTGCGCTTATGGAAAATCGAAAGCCATTTCAGTTAAGAAAAATCATTGTAGTTTA
TAATTTTCTGCAAGTACTACTGAGTGCTTGGCTGTTTTGGGGTTTGGGAAAATCGGGATG
GTTCACAAATTATAGTTACAGATGTCAACCAGTAGATTTATCTTATAGTGCACAAGCCAT
ACAGATGACACACTTTTGTTGGTGGTATTACTTCAGTAAATTTACAGAGTTCTTTGACAC
ATTTTTCTTTGTTTTGAGAAAAAGATATGATCAAGTTTCAACTTTGCATGTAATTCATCA
TGGAATTATGCCTTTTAGTGTATGGTGGGGAGTGAAATTCATGCCTGGCGGTCACAGCAC
CTTCTTTGGACTCCTCAACACATTTGTGCATATCATAATGTATACTTATTATATGTTAGC
TGCAATGGGACCACAAGTTCAAAAATATCTTTGGTGGAAAAAATATCTAACAATTTTGCA
GATGATCCAATTTGTTGGAATTTTTACTCATTGCTTCCAACTGATCTTCCATAATCCCTG
CAATTACTCTTATATTTTTGTATATTGGATTGGTGGTCATGGTGTGCTGTTTTATTTCCT
CTTTAGAAGCTTCTATCAACAAGCTTATGTGGCGAAATCAAAATCAGTAAAAAATGATGA
ACCAAATGACAAAAAGACATTAATTGTAGATGACAATGAAAATATTGTAGAATACAAGAA
ACATTATGAGACAAAAAGAGACTCAATAACACAGATTAATAAGGCACTAGCGAAGCATCT
TTAA

>g12190.t6 Gene=g12190 Length=309
MDALNKISATWQDLMDNKSDPRTTNWFLMSSPLPTVMICLTYVYLVKIVGPALMENRKPF
QLRKIIVVYNFLQVLLSAWLFWGLGKSGWFTNYSYRCQPVDLSYSAQAIQMTHFCWWYYF
SKFTEFFDTFFFVLRKRYDQVSTLHVIHHGIMPFSVWWGVKFMPGGHSTFFGLLNTFVHI
IMYTYYMLAAMGPQVQKYLWWKKYLTILQMIQFVGIFTHCFQLIFHNPCNYSYIFVYWIG
GHGVLFYFLFRSFYQQAYVAKSKSVKNDEPNDKKTLIVDDNENIVEYKKHYETKRDSITQ
INKALAKHL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g12190.t6 PANTHER PTHR11157 FATTY ACID ACYL TRANSFERASE-RELATED 4 281 1.2E-143
3 g12190.t6 PANTHER PTHR11157:SF151 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 4 281 1.2E-143
1 g12190.t6 Pfam PF01151 GNS1/SUR4 family 28 264 1.9E-59
18 g12190.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 25 -
22 g12190.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 26 45 -
13 g12190.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 46 64 -
24 g12190.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 65 82 -
17 g12190.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 83 101 -
20 g12190.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 102 120 -
12 g12190.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 121 140 -
19 g12190.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 141 160 -
16 g12190.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 161 171 -
23 g12190.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 172 192 -
14 g12190.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 193 203 -
21 g12190.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 204 225 -
15 g12190.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 226 230 -
25 g12190.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 231 250 -
11 g12190.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 251 309 -
9 g12190.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 24 46 -
6 g12190.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 66 85 -
5 g12190.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 112 134 -
4 g12190.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 141 160 -
10 g12190.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 170 192 -
8 g12190.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 204 226 -
7 g12190.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 231 253 -

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

Pathway

  • This transcript belongs to the following pathways

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