General information for g15932.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable GDP-L-fucose synthase.
Parent gene
- The parent gene g15932 is located on chr_4: 7466847..7468585 (- strand)
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.t1 | TTS | g15932.t1 | 7466780 | 7466780 |
| chr_4 | g15932 | g15932.t1 | isoform | g15932.t1 | 7466847 | 7468585 |
| chr_4 | g15932 | g15932.t1 | exon | g15932.t1.exon1 | 7466847 | 7467372 |
| chr_4 | g15932 | g15932.t1 | cds | g15932.t1.CDS1 | 7466847 | 7467372 |
| chr_4 | g15932 | g15932.t1 | exon | g15932.t1.exon2 | 7467575 | 7467648 |
| chr_4 | g15932 | g15932.t1 | cds | g15932.t1.CDS2 | 7467575 | 7467648 |
| chr_4 | g15932 | g15932.t1 | exon | g15932.t1.exon3 | 7467869 | 7468112 |
| chr_4 | g15932 | g15932.t1 | cds | g15932.t1.CDS3 | 7467869 | 7468112 |
| chr_4 | g15932 | g15932.t1 | exon | g15932.t1.exon4 | 7468458 | 7468585 |
| chr_4 | g15932 | g15932.t1 | cds | g15932.t1.CDS4 | 7468458 | 7468585 |
| chr_4 | g15932 | g15932.t1 | TSS | g15932.t1 | 7468630 | 7468630 |
Sequences
>g15932.t1 Gene=g15932 Length=972
ATGTCAAAAAAAGTTTTAGTTACAGGTGGTTCAGGTCTTGTTGGTAGTGCAATTAAAAAT
GTTATCAATGAAGAATCACCAGCAGATGAAGTCTGGATATTTTGCAGCTCCAAAGATGCT
GATTTGTGCAATTACGAGTCAACAAAGCAACTTTTTGAGAAACACAAGCCAACTCATGTA
ATTCATTTAGCAGCAATGGTTGGTGGATTGTTTCACAATATGAATGACAATCTTGGATTC
TTTCGTTCTAATATGACAATGAATGACAACATTTTAAAATTATCACATGAATTTGGAGTT
CAAAAAGTTGTTTCGTGTTTATCAACTTGTATTTTTCCTGATAAGACTGAATATCCTATT
GATGAGACTATGGTTCATAATGGTCCACCACATGATTCAAATTTCGGCTACAGCTATGCT
AAAAGAATGATTGATGTTTTAAATAAGGCATATAACCAAAAACACAACTGCAACTTTACT
TCAGTGATTCCATGCAATGTTTTCGGTCCACATGATAATTATAAAGAAGGAGTTTCTCAT
GTAATTCCAGGCATGATTCATCGTCTTCACAAACTTATCAATATTGATAATCCAGAAATA
CCTCAAGAAGAAAAAGAATTTATTGTTTATGGAAGTGGAAAACCTTTGAGACAATTTATT
TATTCACTTGATCTTGCAAAGTTGTTCATTTGGGTGCTAAGAAATTATGACTCAGTTGAG
CCGATAATTTTATCAGTTGATGAAAGTGCTGAAGTGTCAATTGCAAAATTAGCTGAATCA
ATTGCAAAAGCTTTTAATTTTAAAGGAAAAATTGTTTTTGACACAACAAAAGCTGATGGG
CAGTACAAAAAAACTGCATCAAATAAGAAATTGAGAGGACTTTTGCCTGATTTCAAATTT
ACTGATTTTGATGTTGCTATGAAAACTTCTGTTGATTGGTTTATTGAGCATTATGATGAA
GCAAGAAAATAA
>g15932.t1 Gene=g15932 Length=323
MSKKVLVTGGSGLVGSAIKNVINEESPADEVWIFCSSKDADLCNYESTKQLFEKHKPTHV
IHLAAMVGGLFHNMNDNLGFFRSNMTMNDNILKLSHEFGVQKVVSCLSTCIFPDKTEYPI
DETMVHNGPPHDSNFGYSYAKRMIDVLNKAYNQKHNCNFTSVIPCNVFGPHDNYKEGVSH
VIPGMIHRLHKLINIDNPEIPQEEKEFIVYGSGKPLRQFIYSLDLAKLFIWVLRNYDSVE
PIILSVDESAEVSIAKLAESIAKAFNFKGKIVFDTTKADGQYKKTASNKKLRGLLPDFKF
TDFDVAMKTSVDWFIEHYDEARK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g15932.t1 | CDD | cd05239 | GDP_FS_SDR_e | 4 | 315 | 5.12609E-163 |
| 6 | g15932.t1 | Gene3D | G3DSA:3.40.50.720 | - | 5 | 301 | 1.4E-111 |
| 7 | g15932.t1 | Gene3D | G3DSA:3.90.25.10 | - | 169 | 316 | 1.4E-111 |
| 4 | g15932.t1 | Hamap | MF_00956 | GDP-L-fucose synthase [fcl]. | 2 | 316 | 39.121353 |
| 2 | g15932.t1 | PANTHER | PTHR43238:SF1 | GDP-L-FUCOSE SYNTHASE | 2 | 323 | 1.4E-138 |
| 3 | g15932.t1 | PANTHER | PTHR43238 | GDP-L-FUCOSE SYNTHASE | 2 | 323 | 1.4E-138 |
| 1 | g15932.t1 | Pfam | PF01370 | NAD dependent epimerase/dehydratase family | 5 | 240 | 1.5E-55 |
| 9 | g15932.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 17 | - |
| 10 | g15932.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 4 | - |
| 11 | g15932.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 5 | 13 | - |
| 12 | g15932.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 17 | - |
| 8 | g15932.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 18 | 323 | - |
| 5 | g15932.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 1 | 319 | 2.08E-59 |
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:0009226 | nucleotide-sugar biosynthetic process | BP |
| GO:0003824 | catalytic activity | MF |
| GO:0016491 | oxidoreductase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K02377 (GDP-L-fucose synthase)
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.
