General information for g13494.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Beta-1,3-galactosyltransferase 6.
Parent gene
- The parent gene g13494 is located on chr_1: 30510723..30511809 (+ 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_1 | g13494 | g13494.t4 | isoform | g13494.t4 | 30508925 | 30510320 |
| chr_1 | g13494 | g13494.t4 | exon | g13494.t4.exon1 | 30508925 | 30510253 |
| chr_1 | g13494 | g13494.t4 | cds | g13494.t4.CDS1 | 30509074 | 30510219 |
| chr_1 | g13494 | g13494.t4 | exon | g13494.t4.exon2 | 30510318 | 30510320 |
| chr_1 | g13494 | g13494.t4 | TTS | g13494.t4 | 30510719 | 30510719 |
| chr_1 | g13494 | g13494.t4 | TSS | g13494.t4 | NA | NA |
Sequences
>g13494.t4 Gene=g13494 Length=1332
AGTAAGTAAAAATTAACGGTTAGAAATATTTTAAATGCACATACTTACCTATAAAAACTT
TTCAATATGGCAATACTAAATTGAAAGATAGAATAACATTACACGCGAAGTGAAAAAAGA
TTATAATTGATTTTAATTAAGGAAAAGCAATGACAAATTTAAGAAATCGAAAGAAACTGA
TGAAAGCATTACAATTCATAAGTGTCTTCTTTATAGGAATAATTTTTAATCATTTATTTA
GTGAATATAAATGTGACATCAGTAAATTCCATGATAAAGTTGATGAAAATAATTATTTAA
TAGTAGCATTAATTTTAACTGCCCCAAAAAATTTTGATAGAAGAAATGTAATGCGAGAAA
CATGGCTGAGTTTAAGACCGTGGCAATTAAATGATAGTTTTTATCAAAATCAAATAATTT
ACATACCATCAGAACAGAATAATGGCTTTCTAAAGTTAGAAAGTGTACAACAACAAGAGA
GTAGTCTAAAAAATTATCAAAAATGGTTGATGAATAATCATAAAGGTTCAAATGTCAAAG
TGCCAAACTTGAAAATAAAAACATTATTCGCTATCGGCACAAAAGACCTCGATGATGAAA
CAGCGAAAAGAATCAGAGCAGAAAATGATGTTTATAATGATTTGCTTCTGCTCGATGAAC
TCAAAGACTCGTATAAGAATCTCACATTGAAGCTATTAAGTGCATTAGAAAAAGTCAACT
ATGTTACACCCAATTTCAAATATCTTCTCAAATGTGATGATGATTCATATGTGAAGTTAG
ACTATTTAGCATTAGATCTCATAGAATATACCAAAAAGCTAAAAGTCAAACAATTAGAAA
AAAATCTCGAATTATATTGGGGCTTCTTTAATGGTCGTGCGAATATAAAGAAATCGGGTC
AGTGGAAAGAAGTCAATTATAACTTGTGTGATCGTTATTTGCCCTATGCATTAGGCGGTG
GCTATGTAATATCAAAGAATCTCGTTTCATACATTGGCAATCATAGCACAATTTTAAATC
GTTATGAAAGTGAAGATATATCTTTAGGTACATGGCTTTCAACATTCAGAAATATTCATT
GGAGACATGATCCACGTTTTGACACAACTTATATTCCACGAAAATGCCAAAAATATCATA
TTGTAATGCACAAAAGAACAATAACCGATATGCAAGAAATACATAAGGGAAATCATTGTT
TTAGTGAAGTAAAATATGATGAAAACAAAAAACCGTCTGAATATTTTTATGATTGGTCTC
AATTACCATCAAAATGCTGTGATAATAGAATTTAATTTAAATAATAAAACGTATTGTTAA
GTTTTATAGTCT
>g13494.t4 Gene=g13494 Length=381
MTNLRNRKKLMKALQFISVFFIGIIFNHLFSEYKCDISKFHDKVDENNYLIVALILTAPK
NFDRRNVMRETWLSLRPWQLNDSFYQNQIIYIPSEQNNGFLKLESVQQQESSLKNYQKWL
MNNHKGSNVKVPNLKIKTLFAIGTKDLDDETAKRIRAENDVYNDLLLLDELKDSYKNLTL
KLLSALEKVNYVTPNFKYLLKCDDDSYVKLDYLALDLIEYTKKLKVKQLEKNLELYWGFF
NGRANIKKSGQWKEVNYNLCDRYLPYALGGGYVISKNLVSYIGNHSTILNRYESEDISLG
TWLSTFRNIHWRHDPRFDTTYIPRKCQKYHIVMHKRTITDMQEIHKGNHCFSEVKYDENK
KPSEYFYDWSQLPSKCCDNRI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g13494.t4 | Coils | Coil | Coil | 168 | 188 | - |
| 2 | g13494.t4 | PANTHER | PTHR11214:SF226 | BETA-1,3-GALACTOSYLTRANSFERASE 6 | 42 | 325 | 1.4E-48 |
| 3 | g13494.t4 | PANTHER | PTHR11214 | BETA-1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE | 42 | 325 | 1.4E-48 |
| 1 | g13494.t4 | Pfam | PF01762 | Galactosyltransferase | 127 | 305 | 7.7E-28 |
| 6 | g13494.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 11 | - |
| 8 | g13494.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 30 | - |
| 7 | g13494.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 31 | 381 | - |
| 4 | g13494.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 13 | 30 | - |
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:0016020 | membrane | CC |
| GO:0006486 | protein glycosylation | BP |
| GO:0016758 | hexosyltransferase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00734 (galactosylxylosylprotein 3-beta-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.
