Gene loci information

Transcript annotation

  • This transcript has been annotated as Acyl-lipid (8-3)-desaturase.

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 g10460 g10460.t1 TSS g10460.t1 9913358 9913358
chr_1 g10460 g10460.t1 isoform g10460.t1 9913513 9914899
chr_1 g10460 g10460.t1 exon g10460.t1.exon1 9913513 9913651
chr_1 g10460 g10460.t1 cds g10460.t1.CDS1 9913513 9913651
chr_1 g10460 g10460.t1 exon g10460.t1.exon2 9913719 9914899
chr_1 g10460 g10460.t1 cds g10460.t1.CDS2 9913719 9914899
chr_1 g10460 g10460.t1 TTS g10460.t1 9914984 9914984

Sequences

>g10460.t1 Gene=g10460 Length=1320
ATGATTGAAAAGATAAAAATAAAAGATTTGAGAGAGCACTGCACTGAAGAATCGGCATGG
ATTGCAATTCGCAGTAAAGTTTATGACATCACATCGTTTGTCGCTCGTCATCCGGGAGGC
AAAGATCAATTAAGATTCGGAATTGGACGTGATGCGACAACTGTATTCGAGACTTATCAC
AATGTGGAAAATGTGCAACGTGTATTGAATAAATTACCGATTGTTGGTGATTTAATTGAT
TCGGAATTGCCCCAATTTAATGAGGCAAGTGAATTTCACAAGACAATAAATTTAAAAGTA
CGTAAACGCTTTCACGATGCTGGTTTAGACATGAAAAATTCTCACAAAGCATGGCTCACC
TACAGTGTTATTTTTCTTTCGATAACTTTGAGTTTTTATCAACAATATTTCGGATACATG
AGCAATTCAACAATTTTACAAATTCTATGTGCTTCAATCCTTGGATTCTTTTGTGCACAA
TTAGGTTTACATATAATGCACGATGCTTCACATTTTTCTATTACACATAATCCATTGGTA
TGGAAATATCTTGGATCTACTCATGATTTTGTCAATGGTGCAAGTTTCATTGCGTGGATT
TATCAACATACATTTGGTCATCATCCTTATACAAATATTCCAAATGCCGATCCTGATATT
CATGTACAACCTGAGCGTGACTTTCGTCGCATTTTAAATTATCAAAAGTGGTTCAATTAC
TATAAGCTACAACACATTTACGCGCCAATACTTTATGCTGGACTCGGTGTTAAAACAAGA
CTGCAAGATCTGAGGATATTGTACATCCAAAAATCTAATGGGCCAATTTCAGTCAATCCA
TTAACAATTGAGCAAAATATATTAACAATTGGTGGTAAAATATTCTTTATCTTTTATCGA
TTTTTACTGCCTGTTCTATTTGGATTTACGTGGACAAGAGTCTTTGCTCTATTTCTATTA
TCAGACATTGTCACATCATACTGGCTTGCATTGACTTTCCAAGCTAATCATGTTGTTGAA
GAAGTTATGCTTCCATTTCAACAATCAAAAGATGTTGATTGGGCAAAAATGCAAGTAATG
ACAACAGTTGACTATGCAATTAATTCAGTTTTAACTCAATTAGCTGTTGGTTCATTAAAC
TTCCAAACTGTTCATCATCTCTTCCCTGGTGTGCTTCAACATCACTATCCACTTATTCAA
GACATTATTTATGATGAATGTCGAAAAAACAATGTTAAGTACAACACAAAAGAAACTTTG
ATTGAGGCTGTTGCTGCTCATATTCAATTTTTAAAGAATATGGGTGAAAAAGAAATCTGA

>g10460.t1 Gene=g10460 Length=439
MIEKIKIKDLREHCTEESAWIAIRSKVYDITSFVARHPGGKDQLRFGIGRDATTVFETYH
NVENVQRVLNKLPIVGDLIDSELPQFNEASEFHKTINLKVRKRFHDAGLDMKNSHKAWLT
YSVIFLSITLSFYQQYFGYMSNSTILQILCASILGFFCAQLGLHIMHDASHFSITHNPLV
WKYLGSTHDFVNGASFIAWIYQHTFGHHPYTNIPNADPDIHVQPERDFRRILNYQKWFNY
YKLQHIYAPILYAGLGVKTRLQDLRILYIQKSNGPISVNPLTIEQNILTIGGKIFFIFYR
FLLPVLFGFTWTRVFALFLLSDIVTSYWLALTFQANHVVEEVMLPFQQSKDVDWAKMQVM
TTVDYAINSVLTQLAVGSLNFQTVHHLFPGVLQHHYPLIQDIIYDECRKNNVKYNTKETL
IEAVAAHIQFLKNMGEKEI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g10460.t1 CDD cd03506 Delta6-FADS-like 148 412 2.71927E-43
6 g10460.t1 Gene3D G3DSA:3.10.120.10 Flavocytochrome B2 2 92 1.6E-20
3 g10460.t1 PANTHER PTHR19353:SF37 ACYL-LIPID (8-3)-DESATURASE B-RELATED 12 436 1.6E-103
4 g10460.t1 PANTHER PTHR19353 FATTY ACID DESATURASE 2 12 436 1.6E-103
14 g10460.t1 PIRSF PIRSF015921 FA_sphingolip_des 2 439 3.3E-99
2 g10460.t1 Pfam PF00173 Cytochrome b5-like Heme/Steroid binding domain 8 78 1.4E-19
1 g10460.t1 Pfam PF00487 Fatty acid desaturase 148 416 4.5E-33
8 g10460.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 117 -
13 g10460.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 118 138 -
10 g10460.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 139 143 -
12 g10460.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 144 163 -
7 g10460.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 164 296 -
11 g10460.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 297 320 -
9 g10460.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 321 439 -
22 g10460.t1 ProSitePatterns PS00191 Cytochrome b5 family, heme-binding domain signature. 33 40 -
23 g10460.t1 ProSiteProfiles PS50255 Cytochrome b5 family, heme-binding domain profile. 2 79 19.748
21 g10460.t1 SMART SM01117 Cyt_b5_2 5 79 1.7E-19
5 g10460.t1 SUPERFAMILY SSF55856 Cytochrome b5-like heme/steroid binding domain 5 83 3.79E-22
18 g10460.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 117 139 -
20 g10460.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 144 166 -
17 g10460.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 179 201 -
16 g10460.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 287 309 -
19 g10460.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 314 336 -

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:0020037 heme binding MF
GO:0016021 integral component of membrane CC
GO:0016491 oxidoreductase activity MF
GO:0006629 lipid metabolic process BP

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.

Raw TPM values