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.t9 TTS g12190.t9 21658510 21658510
chr_1 g12190 g12190.t9 isoform g12190.t9 21658682 21664654
chr_1 g12190 g12190.t9 exon g12190.t9.exon1 21658682 21659145
chr_1 g12190 g12190.t9 cds g12190.t9.CDS1 21658682 21659145
chr_1 g12190 g12190.t9 exon g12190.t9.exon2 21659328 21659460
chr_1 g12190 g12190.t9 cds g12190.t9.CDS2 21659328 21659460
chr_1 g12190 g12190.t9 exon g12190.t9.exon3 21659571 21659759
chr_1 g12190 g12190.t9 cds g12190.t9.CDS3 21659571 21659759
chr_1 g12190 g12190.t9 exon g12190.t9.exon4 21661922 21662062
chr_1 g12190 g12190.t9 cds g12190.t9.CDS4 21661922 21662062
chr_1 g12190 g12190.t9 exon g12190.t9.exon5 21664628 21664654
chr_1 g12190 g12190.t9 cds g12190.t9.CDS5 21664628 21664630
chr_1 g12190 g12190.t9 TSS g12190.t9 21664861 21664861

Sequences

>g12190.t9 Gene=g12190 Length=954
TCAGAAAGAATTAATAAAAAATAGATGATGGATGCTCTAAACAAAATTAGTGCCACATGG
CAAGACTTAATGGACAACAAGTCCGATCCAAGAACGACAAATTGGTTCCTTATGTCATCG
CCACTTCCCACTGTGATGATCTGCCTTACATATGTTTATTTAGTCAAGATAGTTGGTCCT
GCGCTTATGGAAAATCGAAAGCCATTTCAGTTAAGAAAAATCATTGTAGTTTATAATTTT
CTGCAAGTACTACTGAGTGCTTGGCTGTTTTGGGGTTTGGGAAAATCGGGATGGTTCACA
AATTATAGTTACAGATGTCAACCAGTAGATTTATCTTATAGTGCACAAGCCATACAGATG
ACACACTTTTGTTGGTGGTATTACTTCAGTAAATTTACAGAGTTCTTTGACACATTTTTC
TTTGTTTTGAGAAAAAGATATGATCAAGTTTCAACTTTGCATGTAATTCATCATGGAATT
ATGCCTTTTATATGGTGGGGAGTGAAATTCATGCCTGGCGGTCACAGCACCTTCTTTGGA
CTCCTCAACACATTTGTGCATATCATAATGTATACTTATTATATGTTAGCTGCAATGGGA
CCACAAGTTCAAAAATATCTTTGGTGGAAAAAATATCTAACAATTTTGCAGATGATCCAA
TTTGTTGGAATTTTTACTCATTGCTTCCAACTGATCTTCCATAATCCCTGCAATTACTCT
TATATTTTTGTATATTGGATTGGTGGTCATGGTGTGCTGTTTTATTTCCTCTTTAGAAGC
TTCTATCAACAAGCTTATGTGGCGAAATCAAAATCAGTAAAAAATGATGAACCAAATGAC
AAAAAGACATTAATTGTAGATGACAATGAAAATATTGTAGAATACAAGAAACATTATGAG
ACAAAAAGAGACTCAATAACACAGATTAATAAGGCACTAGCGAAGCATCTTTAA

>g12190.t9 Gene=g12190 Length=309
MMDALNKISATWQDLMDNKSDPRTTNWFLMSSPLPTVMICLTYVYLVKIVGPALMENRKP
FQLRKIIVVYNFLQVLLSAWLFWGLGKSGWFTNYSYRCQPVDLSYSAQAIQMTHFCWWYY
FSKFTEFFDTFFFVLRKRYDQVSTLHVIHHGIMPFIWWGVKFMPGGHSTFFGLLNTFVHI
IMYTYYMLAAMGPQVQKYLWWKKYLTILQMIQFVGIFTHCFQLIFHNPCNYSYIFVYWIG
GHGVLFYFLFRSFYQQAYVAKSKSVKNDEPNDKKTLIVDDNENIVEYKKHYETKRDSITQ
INKALAKHL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g12190.t9 PANTHER PTHR11157 FATTY ACID ACYL TRANSFERASE-RELATED 5 281 1.5E-140
3 g12190.t9 PANTHER PTHR11157:SF151 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 5 281 1.5E-140
1 g12190.t9 Pfam PF01151 GNS1/SUR4 family 29 264 7.3E-58
17 g12190.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 26 -
24 g12190.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 27 46 -
14 g12190.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 47 65 -
22 g12190.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 66 83 -
18 g12190.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 84 102 -
23 g12190.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 103 121 -
12 g12190.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 122 141 -
19 g12190.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 142 160 -
16 g12190.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 161 171 -
21 g12190.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 172 192 -
13 g12190.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 193 203 -
20 g12190.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 204 225 -
15 g12190.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 226 230 -
25 g12190.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 231 250 -
11 g12190.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 251 309 -
9 g12190.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 25 47 -
8 g12190.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 67 86 -
6 g12190.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 113 135 -
4 g12190.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 142 160 -
10 g12190.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 170 192 -
7 g12190.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 204 226 -
5 g12190.t9 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