General information for g16434.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 g16434 is located on chr_4: 9428552..9429412 (+ 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 | g16434 | g16434.t1 | TSS | g16434.t1 | 9427031 | 9427031 |
| chr_4 | g16434 | g16434.t1 | isoform | g16434.t1 | 9427355 | 9429412 |
| chr_4 | g16434 | g16434.t1 | exon | g16434.t1.exon1 | 9427355 | 9427400 |
| chr_4 | g16434 | g16434.t1 | cds | g16434.t1.CDS1 | 9427355 | 9427400 |
| chr_4 | g16434 | g16434.t1 | exon | g16434.t1.exon2 | 9427460 | 9427749 |
| chr_4 | g16434 | g16434.t1 | cds | g16434.t1.CDS2 | 9427460 | 9427749 |
| chr_4 | g16434 | g16434.t1 | exon | g16434.t1.exon3 | 9428552 | 9429412 |
| chr_4 | g16434 | g16434.t1 | cds | g16434.t1.CDS3 | 9428552 | 9429412 |
| chr_4 | g16434 | g16434.t1 | TTS | g16434.t1 | 9429908 | 9429908 |
Sequences
>g16434.t1 Gene=g16434 Length=1197
ATGAATAAATTCAATGACGTTCGATATAAAATGTTAAATAGTGATTCTCATCTACCTATT
CGATCTCATCACATTAATTATTTACGACGTTCAAATTTTGTCATTTTATTCTTTGGTTTT
GCACTTGGCTTCTTTTTTGCCATTCTCATGGAATTTTCACCCAGCACGATGACTTTCAAA
TCCAATGATGCTTTTACATTCAAACATAGTGATCCGCATTTTGGTCGAGAATTAAATGAT
GCTTCTGGACCTACAGCAGATGTTGGATTTCATGAACCGTATGATAATACTCACAAATAT
GAGAATGGAACTGTTGCTAGTCAGCTTTATAAAGATGTCCGTGTATTATGCTGGATTATG
ACAAATCCAAAAAATCATAAAAAGAAAGCAATCCATGTTAAAAAGACTTGGGGAAAACGC
TGTAATAAGTTGCTCTTTATGAGTTCAACAGTTGATCCAGAACTCGAATCAGTGGCACTG
CCAGTTAAAGAAGGTCGTAATAATCTCTGGGCGAAGACCAAAGAAGCTTTTAAGTATATT
TATGATCATCACTTGGATGAAATTGATTGGGTATTAAAAGCTGATGATGACACATATGTT
GTGGTAGAAAATCTTCGATATATGTTATATCCATATGCATCAAGTCAACCTATATATTTT
GGTTGTCGTTTTAAGCCATATGTAAAGCAAGGTTACATGTCAGGTGGTGCAGGATATGTG
CTATCAAAGCAAGCTCTAATAAGATTTGTTGAAGAAGGTCTGACAGATAAAACAAAATGT
CGACAAGATGCTGATGGTGCTGAAGATGTTGAAATCGGCAAGTGCCTCGAAAATGTTCAT
GTCCTTGCTGGTGATTCACGTGATTCTCACGGTCGAGGAAGATTTTTTCCATTTGTACCG
GAACATCATTTAATACCTGGACATGTTGATAAAAATTTTTGGTATTACAAATATATTTAT
TATGAGGCAAAAGAGGGAATGGACTGCTGTTCTGATAATGCAATTTCATTTCATTATGTG
TCACCAAATCAAATGTATGTATTGGAATATTTGATTTATCATTTAAGACCATATGGACTA
GTGCAGTTTGATCAACCGCTGCCAAAGAAAATTTCTTTATCTGAAATTAGTGAAGAAGCT
CATAAAAATGCAACAAATTTAAATGAATCAAACACCAATGATAATGAAAAATTATAA
>g16434.t1 Gene=g16434 Length=398
MNKFNDVRYKMLNSDSHLPIRSHHINYLRRSNFVILFFGFALGFFFAILMEFSPSTMTFK
SNDAFTFKHSDPHFGRELNDASGPTADVGFHEPYDNTHKYENGTVASQLYKDVRVLCWIM
TNPKNHKKKAIHVKKTWGKRCNKLLFMSSTVDPELESVALPVKEGRNNLWAKTKEAFKYI
YDHHLDEIDWVLKADDDTYVVVENLRYMLYPYASSQPIYFGCRFKPYVKQGYMSGGAGYV
LSKQALIRFVEEGLTDKTKCRQDADGAEDVEIGKCLENVHVLAGDSRDSHGRGRFFPFVP
EHHLIPGHVDKNFWYYKYIYYEAKEGMDCCSDNAISFHYVSPNQMYVLEYLIYHLRPYGL
VQFDQPLPKKISLSEISEEAHKNATNLNESNTNDNEKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g16434.t1 | Gene3D | G3DSA:3.90.550.50 | - | 106 | 282 | 4.2E-14 |
| 2 | g16434.t1 | PANTHER | PTHR23033:SF13 | GLYCOPROTEIN-N-ACETYLGALACTOSAMINE 3-BETA-GALACTOSYLTRANSFERASE 1 | 32 | 389 | 7.6E-120 |
| 3 | g16434.t1 | PANTHER | PTHR23033 | BETA1,3-GALACTOSYLTRANSFERASE | 32 | 389 | 7.6E-120 |
| 1 | g16434.t1 | Pfam | PF02434 | Fringe-like | 118 | 279 | 2.5E-11 |
| 6 | g16434.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 32 | - |
| 8 | g16434.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 33 | 52 | - |
| 7 | g16434.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 53 | 398 | - |
| 4 | g16434.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 31 | 50 | - |
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.
