General information for g5688.t1
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.t1 | TTS | g5688.t1 | 11257058 | 11257058 |
| chr_2 | g5688 | g5688.t1 | isoform | g5688.t1 | 11257405 | 11258588 |
| chr_2 | g5688 | g5688.t1 | exon | g5688.t1.exon1 | 11257405 | 11257733 |
| chr_2 | g5688 | g5688.t1 | cds | g5688.t1.CDS1 | 11257405 | 11257733 |
| chr_2 | g5688 | g5688.t1 | exon | g5688.t1.exon2 | 11257795 | 11258235 |
| chr_2 | g5688 | g5688.t1 | cds | g5688.t1.CDS2 | 11257795 | 11258235 |
| chr_2 | g5688 | g5688.t1 | exon | g5688.t1.exon3 | 11258303 | 11258588 |
| chr_2 | g5688 | g5688.t1 | cds | g5688.t1.CDS3 | 11258303 | 11258588 |
| chr_2 | g5688 | g5688.t1 | TSS | g5688.t1 | 11258723 | 11258723 |
Sequences
>g5688.t1 Gene=g5688 Length=1056
ATGAATCTCCGATACATCAATTCAAATATTATAAGAAAGCGAATCTTTTTGTTTCTTGTT
ATTATAGTTTTATTAATAATTTTTGTTTATAGTGTTAGAAATGATGCCAAAAATTGCTTT
TTAAATTACACTTGGACTGATGGAAAAACTTTACAAGATGTCTCAAAAAATATTCACCTT
AAAACACATTCTTCATCCAAAAATATTTTCTTTCACGAAACTTCTTGCAGTAATGATGGA
ATTATTAAAATAAATTCCAGACAAGCTTGTGCTATTGAAAGTGCTGCACGTATGAATCCA
GATTACAACATATATTTACTTTTCACATCACAAGTTGGCTATCGTAATGAAACGCCACTG
CCTCTAGTTGACACTCTTCTTAGTTATCATAATGTTCATTTCAATTATTTAAACATAACT
AGATATGCAGAAAGCACTCCACTTGCAGATTGGATAAAGAATGGAGATTTATTTCGTTCA
AGCTATGTAACATCACATACAAGTGATGTACTTCGTTATTTATCATTATGGAAATATGGA
GGAACTTATATGGACTTGGACATTGTAATGTTAGATAAATTAAGCAAACAAAAACCAAAT
TATGCTGGCGCTGAATCGAACAAATTTGTAGCCGTAGGAATAATTAACTTTGAAGGTGAA
AGTGGTCATGAAATTGCTGATATGTGTCTTAGAGATTTGCTCAAGAATTTTAATGGAGAA
GATTGGGGAAATAATGGTCCAGGCGTGCTTACTCGTGTGTTGCAAAAAATTTGTGGAACA
AAAGATGTAATGAAGATGATGATTGATGGAGTATGTAAAAATTTTAATGTACTCCCAATA
GAAAAGTGTTATAGCATAAGATGGCCTGAACATAGAAAATTCTTTGAAGAAGCTTTCTTA
AATGAAACTCTTGAACGTTTATCTGATTCATTAATTGCTCATGTGTGGAATAAACATAGT
GCCGCTACAGTGTTAACGAAGGAATCAAATGTTGCCTATATACATCTTGCAAAGAAATAT
TGTCCCAAAACTTTATCTGCAAGTGAATTTTTTTAG
>g5688.t1 Gene=g5688 Length=351
MNLRYINSNIIRKRIFLFLVIIVLLIIFVYSVRNDAKNCFLNYTWTDGKTLQDVSKNIHL
KTHSSSKNIFFHETSCSNDGIIKINSRQACAIESAARMNPDYNIYLLFTSQVGYRNETPL
PLVDTLLSYHNVHFNYLNITRYAESTPLADWIKNGDLFRSSYVTSHTSDVLRYLSLWKYG
GTYMDLDIVMLDKLSKQKPNYAGAESNKFVAVGIINFEGESGHEIADMCLRDLLKNFNGE
DWGNNGPGVLTRVLQKICGTKDVMKMMIDGVCKNFNVLPIEKCYSIRWPEHRKFFEEAFL
NETLERLSDSLIAHVWNKHSAATVLTKESNVAYIHLAKKYCPKTLSASEFF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5688.t1 | Gene3D | G3DSA:3.90.550.20 | - | 80 | 293 | 2.1E-10 |
| 3 | g5688.t1 | PANTHER | PTHR12042 | LACTOSYLCERAMIDE 4-ALPHA-GALACTOSYLTRANSFERASE ALPHA- 1,4-GALACTOSYLTRANSFERASE | 24 | 347 | 1.1E-80 |
| 1 | g5688.t1 | Pfam | PF04488 | Glycosyltransferase sugar-binding region containing DXD motif | 86 | 196 | 1.1E-17 |
| 2 | g5688.t1 | Pfam | PF04572 | Alpha 1,4-glycosyltransferase conserved region | 220 | 347 | 4.8E-39 |
| 7 | g5688.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 14 | - |
| 9 | g5688.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 15 | 32 | - |
| 8 | g5688.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 33 | 351 | - |
| 5 | g5688.t1 | SUPERFAMILY | SSF53448 | Nucleotide-diphospho-sugar transferases | 52 | 348 | 8.44E-40 |
| 4 | g5688.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 13 | 32 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5688/g5688.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5688.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K01988 (lactosylceramide 4-alpha-galactosyltransferase)
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.
