General information for g5688.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Lactosylceramide 4-alpha-galactosyltransferase.
Parent gene
- The parent gene g5688 is located on chr_2: 11258588..11263934 (- 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_2 | g5688 | g5688.t6 | TTS | g5688.t6 | 11257058 | 11257058 |
| chr_2 | g5688 | g5688.t6 | isoform | g5688.t6 | 11257405 | 11258588 |
| chr_2 | g5688 | g5688.t6 | exon | g5688.t6.exon1 | 11257405 | 11257733 |
| chr_2 | g5688 | g5688.t6 | cds | g5688.t6.CDS1 | 11257405 | 11257733 |
| chr_2 | g5688 | g5688.t6 | exon | g5688.t6.exon2 | 11257795 | 11258328 |
| chr_2 | g5688 | g5688.t6 | cds | g5688.t6.CDS2 | 11257795 | 11258230 |
| chr_2 | g5688 | g5688.t6 | exon | g5688.t6.exon3 | 11258532 | 11258588 |
| chr_2 | g5688 | g5688.t6 | TSS | g5688.t6 | 11258723 | 11258723 |
Sequences
>g5688.t6 Gene=g5688 Length=920
ATGAATCTCCGATACATCAATTCAAATATTATAAGAAAGCGAATCTTTTTGTTTCTTACA
AGCTTGTGCTATTGAAAGTGCTGGTATGTGAGATGTTACGATTATTTCATATGAATGACT
ATTTATTTCTTTATTACTTGATTATTCTAGCACGTATGAATCCAGATTACAACATATATT
TACTTTTCACATCACAAGTTGGCTATCGTAATGAAACGCCACTGCCTCTAGTTGACACTC
TTCTTAGTTATCATAATGTTCATTTCAATTATTTAAACATAACTAGATATGCAGAAAGCA
CTCCACTTGCAGATTGGATAAAGAATGGAGATTTATTTCGTTCAAGCTATGTAACATCAC
ATACAAGTGATGTACTTCGTTATTTATCATTATGGAAATATGGAGGAACTTATATGGACT
TGGACATTGTAATGTTAGATAAATTAAGCAAACAAAAACCAAATTATGCTGGCGCTGAAT
CGAACAAATTTGTAGCCGTAGGAATAATTAACTTTGAAGGTGAAAGTGGTCATGAAATTG
CTGATATGTGTCTTAGAGATTTGCTCAAGAATTTTAATGGAGAAGATTGGGGAAATAATG
GTCCAGGCGTGCTTACTCGTGTGTTGCAAAAAATTTGTGGAACAAAAGATGTAATGAAGA
TGATGATTGATGGAGTATGTAAAAATTTTAATGTACTCCCAATAGAAAAGTGTTATAGCA
TAAGATGGCCTGAACATAGAAAATTCTTTGAAGAAGCTTTCTTAAATGAAACTCTTGAAC
GTTTATCTGATTCATTAATTGCTCATGTGTGGAATAAACATAGTGCCGCTACAGTGTTAA
CGAAGGAATCAAATGTTGCCTATATACATCTTGCAAAGAAATATTGTCCCAAAACTTTAT
CTGCAAGTGAATTTTTTTAG
>g5688.t6 Gene=g5688 Length=254
MNPDYNIYLLFTSQVGYRNETPLPLVDTLLSYHNVHFNYLNITRYAESTPLADWIKNGDL
FRSSYVTSHTSDVLRYLSLWKYGGTYMDLDIVMLDKLSKQKPNYAGAESNKFVAVGIINF
EGESGHEIADMCLRDLLKNFNGEDWGNNGPGVLTRVLQKICGTKDVMKMMIDGVCKNFNV
LPIEKCYSIRWPEHRKFFEEAFLNETLERLSDSLIAHVWNKHSAATVLTKESNVAYIHLA
KKYCPKTLSASEFF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5688.t6 | Gene3D | G3DSA:3.90.550.20 | - | 1 | 212 | 0 |
| 3 | g5688.t6 | PANTHER | PTHR12042 | LACTOSYLCERAMIDE 4-ALPHA-GALACTOSYLTRANSFERASE ALPHA- 1,4-GALACTOSYLTRANSFERASE | 2 | 250 | 0 |
| 1 | g5688.t6 | Pfam | PF04488 | Glycosyltransferase sugar-binding region containing DXD motif | 2 | 99 | 0 |
| 2 | g5688.t6 | Pfam | PF04572 | Alpha 1,4-glycosyltransferase conserved region | 123 | 250 | 0 |
| 4 | g5688.t6 | SUPERFAMILY | SSF53448 | Nucleotide-diphospho-sugar transferases | 1 | 251 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5688/g5688.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5688.t6.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
