Gene loci information

Transcript annotation

  • This transcript has been annotated as Elongation of very long chain fatty acids protein 4.

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_3 g3216 g3216.t2 isoform g3216.t2 23702084 23709168
chr_3 g3216 g3216.t2 exon g3216.t2.exon1 23702084 23702247
chr_3 g3216 g3216.t2 cds g3216.t2.CDS1 23702084 23702247
chr_3 g3216 g3216.t2 exon g3216.t2.exon2 23703168 23703330
chr_3 g3216 g3216.t2 cds g3216.t2.CDS2 23703168 23703330
chr_3 g3216 g3216.t2 exon g3216.t2.exon3 23703648 23703819
chr_3 g3216 g3216.t2 cds g3216.t2.CDS3 23703648 23703819
chr_3 g3216 g3216.t2 exon g3216.t2.exon4 23704342 23704469
chr_3 g3216 g3216.t2 cds g3216.t2.CDS4 23704342 23704469
chr_3 g3216 g3216.t2 exon g3216.t2.exon5 23704530 23704637
chr_3 g3216 g3216.t2 cds g3216.t2.CDS5 23704530 23704637
chr_3 g3216 g3216.t2 exon g3216.t2.exon6 23709028 23709168
chr_3 g3216 g3216.t2 cds g3216.t2.CDS6 23709028 23709168
chr_3 g3216 g3216.t2 TSS g3216.t2 NA NA
chr_3 g3216 g3216.t2 TTS g3216.t2 NA NA

Sequences

>g3216.t2 Gene=g3216 Length=876
ATGGCAAGTTTAGTGAGAAGAATTCAAGATTATTACAACTGGACGCTTACATTAACTGAT
CCACGTTCAAAAGGATGGTTGCTAGTTGATTCACCGTGGCCAACATTATTTGGAATTTCT
GGTTATTTATTGATGGTGTGGTTAGGACCAAAATTCATGAAAAATCGCAAACCTTTAAAA
CTCAACAAACTGCTTGTAGTGTATAATCTTGCCATGGCTGTTCTCAACTTTTATATTTTC
TGGCAGCTGGCTACAGCATCATTAAGACTGAATTACAGTATCTTTTGTGAACCATGTCGA
CAAGTGTGGACACCCAATGAGATGCAGATAGTAAAAGCTGTCTGGTGGTATTATTTTTCA
AAACTACTTGAGTTCAGTGACACACTCTTCTTTATATTGAGGAAAAAGGACAATCAGTTA
TCGTTCCTACACATCTATCATCATTCTACAATGTTTGGCTTCTGGTGGATTGGAGTAAAG
TGGGTGCCAAGCGGTTCGACCGCAATGCCTGCAATTGTTAACTCATTTATTCATGTATTG
ATGTATACTTACTATGGATTGTCTGCTATTGGACCACATATGAATAAATATCTATGGTGG
AAGCGATATTTGACCATTATTCAACTTATACAATTTGCTGGCGCACTCATTCTTGGCTTC
AACGGACTTCGCATTGATTGCGATTTTCCATTATGGATGCAATACACTCTCTGCGGATAT
ATGGTTTCATTCTTGGTTCTTTTTGGACGCTTCTATGTTAACGAGTACATTGAGGATCAC
AAAAAGCGACAAAAGGAGAAACTTTTATCTAACAACAATAATGTTGATACGATAAAAAAT
AAAAATGTCACACTCAATGGAAAGAAGCATGAATAA

>g3216.t2 Gene=g3216 Length=291
MASLVRRIQDYYNWTLTLTDPRSKGWLLVDSPWPTLFGISGYLLMVWLGPKFMKNRKPLK
LNKLLVVYNLAMAVLNFYIFWQLATASLRLNYSIFCEPCRQVWTPNEMQIVKAVWWYYFS
KLLEFSDTLFFILRKKDNQLSFLHIYHHSTMFGFWWIGVKWVPSGSTAMPAIVNSFIHVL
MYTYYGLSAIGPHMNKYLWWKRYLTIIQLIQFAGALILGFNGLRIDCDFPLWMQYTLCGY
MVSFLVLFGRFYVNEYIEDHKKRQKEKLLSNNNNVDTIKNKNVTLNGKKHE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g3216.t2 PANTHER PTHR11157 FATTY ACID ACYL TRANSFERASE-RELATED 5 267 3.1E-106
3 g3216.t2 PANTHER PTHR11157:SF12 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 4 5 267 3.1E-106
1 g3216.t2 Pfam PF01151 GNS1/SUR4 family 28 263 9.5E-63
15 g3216.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 30 -
24 g3216.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 31 49 -
14 g3216.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 50 60 -
25 g3216.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 61 81 -
18 g3216.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 82 114 -
21 g3216.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 115 133 -
13 g3216.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 134 139 -
20 g3216.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 140 159 -
17 g3216.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 160 170 -
23 g3216.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 171 191 -
12 g3216.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 192 202 -
19 g3216.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 203 220 -
16 g3216.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 221 231 -
22 g3216.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 232 253 -
11 g3216.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 254 291 -
9 g3216.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 26 48 -
8 g3216.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 61 83 -
4 g3216.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 114 133 -
7 g3216.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 140 159 -
5 g3216.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 169 191 -
10 g3216.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 203 225 -
6 g3216.t2 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