General information for g1140.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Polypeptide N-acetylgalactosaminyltransferase 1.
Parent gene
- The parent gene g1140 is located on chr_3: 8383259..8385510 (- 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_3 | g1140 | g1140.t4 | isoform | g1140.t4 | 8382620 | 8384293 |
| chr_3 | g1140 | g1140.t4 | exon | g1140.t4.exon1 | 8382620 | 8383362 |
| chr_3 | g1140 | g1140.t4 | TTS | g1140.t4 | 8382645 | 8382645 |
| chr_3 | g1140 | g1140.t4 | cds | g1140.t4.CDS1 | 8383259 | 8383362 |
| chr_3 | g1140 | g1140.t4 | exon | g1140.t4.exon2 | 8383421 | 8383536 |
| chr_3 | g1140 | g1140.t4 | cds | g1140.t4.CDS2 | 8383421 | 8383536 |
| chr_3 | g1140 | g1140.t4 | exon | g1140.t4.exon3 | 8383613 | 8383698 |
| chr_3 | g1140 | g1140.t4 | cds | g1140.t4.CDS3 | 8383613 | 8383698 |
| chr_3 | g1140 | g1140.t4 | exon | g1140.t4.exon4 | 8383774 | 8384034 |
| chr_3 | g1140 | g1140.t4 | cds | g1140.t4.CDS4 | 8383774 | 8384034 |
| chr_3 | g1140 | g1140.t4 | exon | g1140.t4.exon5 | 8384114 | 8384293 |
| chr_3 | g1140 | g1140.t4 | cds | g1140.t4.CDS5 | 8384114 | 8384281 |
| chr_3 | g1140 | g1140.t4 | TSS | g1140.t4 | NA | NA |
Sequences
>g1140.t4 Gene=g1140 Length=1386
GAAAATCTGGAAATGAGTTTTCGAATCTGGATGTGCGGTGGAACATTAGAAACAATTCCT
TGCAGTCGAATTGGACACATTTTTAGAGAGTTTCATCCATATAGCTTTCCAAATGACAAA
GATACTCACGGAATCAATACAGTTCGAATGGCAAAAGTTTGGATGGACGATTATCAAGAG
CTTCTTTATATGAATAGACCTGATTTGAGAAATCATCCTGATGTAGGCGACGTGACACAC
AGAAAAGTATTGAGAGATAAACTTAAGTGCAAATCCTTTGAATGGTATATGCAAAATATA
TACCCTGAAAAATTCATTCCAACAAGAAATGTTCAAAATTATGGACGAATATCAGCTATA
GAAGACGATCGATTTTGCTTTGATGATTTACAACAGAATATTGATGAGCCATATAATTTA
GGAGTTTATTCATGCTATAAGCATGATATTGCACCATCACAACTTTTCTCTTATACTTAT
AATAAAGTATTACGAACAGAAAGAAGTTGTGCAACTATCGATGATCGACGAAGCACTAAA
TATATTGTGATGATTCCTTGCAATAGTGACGATGAAGTTACAGATACTTGGGTTCATACT
AGTTTTAATCAATTTAAACATGAACAAACGGGTCTTTGCATAGATCGAAAAAATTTGGAT
AAAAATTTACTTCATGCAGCTGTATGTGATTCATTATCAAAAACACAAAAATGGGAATTT
CAAAAGACAAAAAAGCAGAGCATTTAGAATCTCATGACTTTTTATATTAGATGTATATCG
TTGTTACTTAAAACTATTTTGTTGGACTTTATTAAACTTATGCATACACACTGACAAACA
TTTACCGTCCGTTCGTTCAGTGACTTTTATCAATTGATGGAACTTTTTTGCTGCTTCACA
AACAACGAATTTAAATGTGAACAAAAAAAATCAATTTCTTGCTTGAAAAAGAGGGAGAAA
AGAAAAGAAAATTTCGTGTCTAACGTCTATGAGCTAAAACTAATGACTTAAATTGATAAC
AAATTAAACTTTTTTATGGTAAATGTTGTACATAATGAGTAAAAGATCTGTTTAAATTAT
TAAGAACAAAAATTTTATTGAAACGAACTTATTAACATTTTGAGTATTCAACATGCACTT
GAGAAAAAATAAAGTTTTAGGTATATTTTTGATGTCGAATAATTAAATTAAAAGTGCCAG
AAAATCCCAAATTAACATATTAGATAGATCAAAAAAGAAAATCAATTCTTTGGGAATGCT
TATAAAAAATTGATACTTAAAGCCACTCTAAATTTGATAACACTAAAATGCTTTTTGTTA
TTTTTAATAAAGAAAGAAGAGAGAGATGTGCAAATAAATAAATAAAATATTGAATTATTT
TATTTT
>g1140.t4 Gene=g1140 Length=244
MSFRIWMCGGTLETIPCSRIGHIFREFHPYSFPNDKDTHGINTVRMAKVWMDDYQELLYM
NRPDLRNHPDVGDVTHRKVLRDKLKCKSFEWYMQNIYPEKFIPTRNVQNYGRISAIEDDR
FCFDDLQQNIDEPYNLGVYSCYKHDIAPSQLFSYTYNKVLRTERSCATIDDRRSTKYIVM
IPCNSDDEVTDTWVHTSFNQFKHEQTGLCIDRKNLDKNLLHAAVCDSLSKTQKWEFQKTK
KQSI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g1140.t4 | CDD | cd00161 | RICIN | 111 | 236 | 0.000000 |
| 8 | g1140.t4 | Gene3D | G3DSA:3.90.550.10 | Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A | 1 | 99 | 0.000000 |
| 7 | g1140.t4 | Gene3D | G3DSA:2.80.10.50 | - | 109 | 242 | 0.000000 |
| 2 | g1140.t4 | PANTHER | PTHR11675 | N-ACETYLGALACTOSAMINYLTRANSFERASE | 1 | 242 | 0.000000 |
| 3 | g1140.t4 | PANTHER | PTHR11675:SF43 | POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 1 | 1 | 242 | 0.000000 |
| 1 | g1140.t4 | Pfam | PF00652 | Ricin-type beta-trefoil lectin domain | 110 | 234 | 0.000000 |
| 9 | g1140.t4 | ProSiteProfiles | PS50231 | Lectin domain of ricin B chain profile. | 109 | 237 | 14.472000 |
| 6 | g1140.t4 | SMART | SM00458 | ricin_3 | 108 | 237 | 0.000015 |
| 5 | g1140.t4 | SUPERFAMILY | SSF53448 | Nucleotide-diphospho-sugar transferases | 1 | 99 | 0.000000 |
| 4 | g1140.t4 | SUPERFAMILY | SSF50370 | Ricin B-like lectins | 94 | 237 | 0.000000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
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.
