General information for g15416.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1.
Parent gene
- The parent gene g15416 is located on chr_4: 5373639..5375392 (- 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 | g15416 | g15416.t1 | isoform | g15416.t1 | 5372373 | 5373639 |
| chr_4 | g15416 | g15416.t1 | exon | g15416.t1.exon1 | 5372373 | 5373242 |
| chr_4 | g15416 | g15416.t1 | cds | g15416.t1.CDS1 | 5372373 | 5373242 |
| chr_4 | g15416 | g15416.t1 | exon | g15416.t1.exon2 | 5373370 | 5373639 |
| chr_4 | g15416 | g15416.t1 | cds | g15416.t1.CDS2 | 5373370 | 5373639 |
| chr_4 | g15416 | g15416.t1 | TSS | g15416.t1 | 5373690 | 5373690 |
| chr_4 | g15416 | g15416.t1 | TTS | g15416.t1 | NA | NA |
Sequences
>g15416.t1 Gene=g15416 Length=1140
ATGAGATATCAAAATCAGTCGACAAGAATATCAAAAGCAATTCCACTATTTTTTGGGTTT
TCATTAGGTTTCTTTCTTGCTTTTCTCATGCAATTTTTGCCAAATATTATAAGAAATGAT
TCTTATAGTGAATATCTTTTCAAACGCAATACTTTGGATTTTCATCATGACAGTTCATTT
GAAGATTTGATTGAATATAAATTTCATGAAGTGAATGATACAACACATAAAAATGACAAT
AATTCAATTGCAAAGCAGCTTTACAATGAGGTACGAGTTTTATGTTGGATTATGACAAAC
CCAGAAAATCATGAAAAGAAAGCAATTCATGTAAAAAATACATGGGGAAAGCATTGTAAT
AAAATTCTTTTCATGAGTTCATCTTATGACAAAAATCTTCCAACAATTGCATTACCAGTC
AAAGAAGGTCGCAATAATCTTTGGGCGAAGACAAAAGAAGCTTTTAAATATGTGTACAAA
AATCATTTAAATGATTTTGATTGGTTTATGAAAGCTGATGATGATACTTATGTGATTGTT
GAAAATTTAAGATATTTTCTTTATCCATATTCATCATATCAGCCAATTTATTTTGGTTGC
CATTTTGATCGTTATATAAAGCAAGGATATATGAGTGGAGGTGCTGGATATGTTTTGAGC
AAAGAAGCACTCAAAAGATTTATTGAAAAAGCACTTCCAAATAAGACTAAATGCAGACAA
GAATCAGATGGTGCTGAAGATGTAGAATTGGGAAAATGTATGGAGAATGTTCAAGTTGAA
GCTGGATATTCACTCGATTCAAGCGGAAAAGGTAGATTCTTTCCAATGGGTCCTGAAAGT
CATTTTAGTCCTGGTTTAATTGATAAAGAATTTTGGTATTATAAATATGTCGATCGTGTG
GGAAGACATGGACTCGATTGTTGTTCTGATTATGCAATTTCCTTTCATTATGTGAGCCCA
GTTCAAATGTATATTTTTGAATATTTTATTTATCATTTAAGACCATATGGGATTACATAT
CAAAATCAACCATTGCCTGAAAAAATTAAAAACAAAAAAAATAATGAAGAAATTTTTATA
AATTTAGGAAGTTTTAATATTTCAAAATTAGAAAAGAAAAATTTTTCTACAATAACATAA
>g15416.t1 Gene=g15416 Length=379
MRYQNQSTRISKAIPLFFGFSLGFFLAFLMQFLPNIIRNDSYSEYLFKRNTLDFHHDSSF
EDLIEYKFHEVNDTTHKNDNNSIAKQLYNEVRVLCWIMTNPENHEKKAIHVKNTWGKHCN
KILFMSSSYDKNLPTIALPVKEGRNNLWAKTKEAFKYVYKNHLNDFDWFMKADDDTYVIV
ENLRYFLYPYSSYQPIYFGCHFDRYIKQGYMSGGAGYVLSKEALKRFIEKALPNKTKCRQ
ESDGAEDVELGKCMENVQVEAGYSLDSSGKGRFFPMGPESHFSPGLIDKEFWYYKYVDRV
GRHGLDCCSDYAISFHYVSPVQMYIFEYFIYHLRPYGITYQNQPLPEKIKNKKNNEEIFI
NLGSFNISKLEKKNFSTIT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g15416.t1 | Gene3D | G3DSA:3.90.550.50 | - | 81 | 261 | 6.4E-15 |
| 2 | g15416.t1 | PANTHER | PTHR23033:SF13 | GLYCOPROTEIN-N-ACETYLGALACTOSAMINE 3-BETA-GALACTOSYLTRANSFERASE 1 | 16 | 356 | 2.4E-114 |
| 3 | g15416.t1 | PANTHER | PTHR23033 | BETA1,3-GALACTOSYLTRANSFERASE | 16 | 356 | 2.4E-114 |
| 1 | g15416.t1 | Pfam | PF02434 | Fringe-like | 97 | 259 | 2.9E-12 |
| 7 | g15416.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 11 | - |
| 9 | g15416.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 33 | - |
| 8 | g15416.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 34 | 379 | - |
| 5 | g15416.t1 | SUPERFAMILY | SSF53187 | Zn-dependent exopeptidases | 176 | 336 | 5.4E-5 |
| 4 | g15416.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.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016020 | membrane | CC |
| GO:0016757 | glycosyltransferase activity | MF |
| GO:0016266 | O-glycan processing | BP |
| GO:0016263 | glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00731 (glycoprotein-N-acetylgalactosamine 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. There were no conditions that were differentially expressed