Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable GDP-L-fucose synthase.

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_4 g15932 g15932.t4 TTS g15932.t4 7466780 7466780
chr_4 g15932 g15932.t4 isoform g15932.t4 7466847 7468585
chr_4 g15932 g15932.t4 exon g15932.t4.exon1 7466847 7467372
chr_4 g15932 g15932.t4 cds g15932.t4.CDS1 7466847 7467372
chr_4 g15932 g15932.t4 exon g15932.t4.exon2 7467575 7468112
chr_4 g15932 g15932.t4 cds g15932.t4.CDS2 7467575 7467594
chr_4 g15932 g15932.t4 exon g15932.t4.exon3 7468458 7468585
chr_4 g15932 g15932.t4 TSS g15932.t4 7468630 7468630

Sequences

>g15932.t4 Gene=g15932 Length=1192
ATGTCAAAAAAAGTTTTAGTTACAGGTGGTTCAGGTCTTGTTGGTAGTGCAATTAAAAAT
GTTATCAATGAAGAATCACCAGCAGATGAAGTCTGGATATTTTGCAGCTCCAAAGATGCT
GATTTGTGCAATTACGAGTCAACAAAGCAACTTTTTGAGAAACACAAGCCAACTCATGTA
ATTCATTTAGCAGCAATGGTTGGTGGATTGTTTCACAATATGAATGACAATCTTGGATTC
TTTCGTTCTAATATGACAATGAATGACAACATTTTAAAATTATCACATGAATTTGGAGTT
CAAAAAGTTGTTTCGTGTTTATCAACTTGTATTTTTCCTGATAAGACTGAATATCCTATT
GATGAGACTATGGTAAGTTAGATCATTTCAAAAGTTTGGTTTAAAAATTGCGGTTTTGAG
TTTTTAAGTAAAAGCTTTATAGATTTAAATTTTAAATTAACAAAATCAAAATTGCTTTTA
ACAAATATTGATCTATTTTTGTCTTTTCTTTCTAATATTTTACTATAAATAAAATCTTAA
CAATTCCTTTTAATTCTTAATTAATTTAAAACAATTTTAAAATATATTCAAGGTTCATAA
TGGTCCACCACATGATTCAAATTTCGGCTACAGCTATGCTAAAAGAATGATTGATGTTTT
AAATAAGGCATATAACCAAAAACACAACTGCAACTTTACTTCAGTGATTCCATGCAATGT
TTTCGGTCCACATGATAATTATAAAGAAGGAGTTTCTCATGTAATTCCAGGCATGATTCA
TCGTCTTCACAAACTTATCAATATTGATAATCCAGAAATACCTCAAGAAGAAAAAGAATT
TATTGTTTATGGAAGTGGAAAACCTTTGAGACAATTTATTTATTCACTTGATCTTGCAAA
GTTGTTCATTTGGGTGCTAAGAAATTATGACTCAGTTGAGCCGATAATTTTATCAGTTGA
TGAAAGTGCTGAAGTGTCAATTGCAAAATTAGCTGAATCAATTGCAAAAGCTTTTAATTT
TAAAGGAAAAATTGTTTTTGACACAACAAAAGCTGATGGGCAGTACAAAAAAACTGCATC
AAATAAGAAATTGAGAGGACTTTTGCCTGATTTCAAATTTACTGATTTTGATGTTGCTAT
GAAAACTTCTGTTGATTGGTTTATTGAGCATTATGATGAAGCAAGAAAATAA

>g15932.t4 Gene=g15932 Length=181
MIDVLNKAYNQKHNCNFTSVIPCNVFGPHDNYKEGVSHVIPGMIHRLHKLINIDNPEIPQ
EEKEFIVYGSGKPLRQFIYSLDLAKLFIWVLRNYDSVEPIILSVDESAEVSIAKLAESIA
KAFNFKGKIVFDTTKADGQYKKTASNKKLRGLLPDFKFTDFDVAMKTSVDWFIEHYDEAR
K

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g15932.t4 Gene3D G3DSA:3.90.25.10 - 27 100 0
6 g15932.t4 Gene3D G3DSA:3.90.25.10 - 104 181 0
2 g15932.t4 PANTHER PTHR43238:SF1 GDP-L-FUCOSE SYNTHASE 1 181 0
3 g15932.t4 PANTHER PTHR43238 GDP-L-FUCOSE SYNTHASE 1 181 0
1 g15932.t4 Pfam PF01370 NAD dependent epimerase/dehydratase family 2 98 0
4 g15932.t4 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 3 177 0

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:0003824 catalytic activity MF

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. There were no conditions that were differentially expressed