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_3 g3955 g3955.t7 isoform g3955.t7 29255622 29256417
chr_3 g3955 g3955.t7 exon g3955.t7.exon1 29255622 29255682
chr_3 g3955 g3955.t7 cds g3955.t7.CDS1 29255622 29255682
chr_3 g3955 g3955.t7 exon g3955.t7.exon2 29255789 29255979
chr_3 g3955 g3955.t7 cds g3955.t7.CDS2 29255789 29255979
chr_3 g3955 g3955.t7 exon g3955.t7.exon3 29256041 29256417
chr_3 g3955 g3955.t7 cds g3955.t7.CDS3 29256041 29256415
chr_3 g3955 g3955.t7 TTS g3955.t7 29257426 29257426
chr_3 g3955 g3955.t7 TSS g3955.t7 NA NA

Sequences

>g3955.t7 Gene=g3955 Length=629
ATGGCTCACTTATTAACAGACCTGTACGATTGGTACAATGACTTGATGGACAATCGTTCA
GATTCTCGTGTCAAAGATTGGCCAATGATGCAGTCACCAATCCCAACATTACTGCTCTGC
ATGAGTTACGCATTTTTCTGTAAATCACTGGCTCCCCGCCTGATGAAAAATCGCAAACCA
TTTGATCTTAGAAAAACTCTAGTTGTATACAATCTGTTTCAAACAGTATTCAGTGCATGG
ATATTTTATGAGTATTTACAAAGTGGTTGGCTGCGTGATTATAGCTATAGATGTCAACCA
GTCGATTATTCGCCTAAAGGATTTAGAATGGCTGAAACATGCTGGTGGTACTACATCTCC
AAATTTACAGAGTTCTTCGATACATTTTTCTTCATACTGAGGAAAAAATATCAACATGTT
TCAACCCTTCATGTCATTCATCACGGTGTTATGCCATTCAGTGTATGGATGGGAATGAAG
TTCGCTCCGGGCGGTCACAGTACCTTTTTTGCAATGCTCAATGCTTTTGTACATATTGTC
ATGTATTTTTATTACATGCTGGCTGCAATGGGTCCACAAGTGCAGAAATATTTATGGTGG
AAGCGATATTTAACGGCGTTTCAAATGGT

>g3955.t7 Gene=g3955 Length=209
MAHLLTDLYDWYNDLMDNRSDSRVKDWPMMQSPIPTLLLCMSYAFFCKSLAPRLMKNRKP
FDLRKTLVVYNLFQTVFSAWIFYEYLQSGWLRDYSYRCQPVDYSPKGFRMAETCWWYYIS
KFTEFFDTFFFILRKKYQHVSTLHVIHHGVMPFSVWMGMKFAPGGHSTFFAMLNAFVHIV
MYFYYMLAAMGPQVQKYLWWKRYLTAFQM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g3955.t7 PANTHER PTHR11157 FATTY ACID ACYL TRANSFERASE-RELATED 3 209 1.2E-107
3 g3955.t7 PANTHER PTHR11157:SF151 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 3 209 1.2E-107
1 g3955.t7 Pfam PF01151 GNS1/SUR4 family 29 209 3.5E-53
13 g3955.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 26 -
19 g3955.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 27 46 -
9 g3955.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 47 66 -
18 g3955.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 67 86 -
12 g3955.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 87 114 -
17 g3955.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 115 133 -
11 g3955.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 134 144 -
16 g3955.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 145 162 -
14 g3955.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 163 167 -
15 g3955.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 168 187 -
10 g3955.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 188 209 -
8 g3955.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 27 46 -
7 g3955.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 67 86 -
4 g3955.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 114 133 -
6 g3955.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 140 159 -
5 g3955.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 169 191 -

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.

Raw TPM values