General information for g17454.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as N-acetylgalactosaminyltransferase 6.
Parent gene
- The parent gene g17454 is located on chr_4: 13578154..13581271 (+ 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 | g17454 | g17454.t2 | isoform | g17454.t2 | 13578154 | 13581271 |
| chr_4 | g17454 | g17454.t2 | exon | g17454.t2.exon1 | 13578154 | 13578269 |
| chr_4 | g17454 | g17454.t2 | exon | g17454.t2.exon2 | 13578968 | 13579826 |
| chr_4 | g17454 | g17454.t2 | exon | g17454.t2.exon3 | 13580060 | 13580190 |
| chr_4 | g17454 | g17454.t2 | cds | g17454.t2.CDS1 | 13580121 | 13580190 |
| chr_4 | g17454 | g17454.t2 | exon | g17454.t2.exon4 | 13580255 | 13580405 |
| chr_4 | g17454 | g17454.t2 | cds | g17454.t2.CDS2 | 13580255 | 13580405 |
| chr_4 | g17454 | g17454.t2 | exon | g17454.t2.exon5 | 13580563 | 13581271 |
| chr_4 | g17454 | g17454.t2 | cds | g17454.t2.CDS3 | 13580563 | 13581271 |
| chr_4 | g17454 | g17454.t2 | TSS | g17454.t2 | NA | NA |
| chr_4 | g17454 | g17454.t2 | TTS | g17454.t2 | NA | NA |
Sequences
>g17454.t2 Gene=g17454 Length=1966
TTTCTTTTATTAAATAATTTTTAATTTTTATAATGGTGTAAATTAGTTCATAATATTATT
GAAAAATGTCAACAAGAAGATTTTTTAGTAAAATTAAACAATTTTTAACATGTCGTTCAC
GACGAGGAATAATTGAAGCTCTTTTAGTTCTTTTTACTTTCATCACTTTAACACTTTTTG
TGATGGTTAAAGTAATAGAAATAAACAATAATCCACTACAAATAAGACAAAATTTTATCT
ACATTGAGCCACTGTCCTCATTTTTCCGTCATACACATAATAAAGAAAATATCAAAATAG
ATTGGCATGATTATAAATTCATAGATGAAGAAAGCACAAGAGAAGGTCCAGGAGAGCATG
GTAGTGCATATAATCAGATTTCAGTAGAAGAAGAAAATTTAAATCAAAGACTATTTGATG
AAAACGGTTATTATGGATTAATATCTGATAAAATTTCAATCAATCGAAGTGTGGCTGACC
TGAGACATACAGATTGTTGGAAAATGAGATATTTGAAAGAATTACCAACAGTTTCTGTGA
TTATTCCATTTTACAATGAACATTTAAGTACTTTATTAAGAACAGTTCATTCAGTCATCA
ACAGAAGTCCATCAAATTTACTTAAAGAAGTAATTTTAATCAATGACAGATCAACAAAAG
AATTTTTATATGATGAACTTCGAACTTACATAGCAGACACATTTAAACCAAATTTTGTGA
AACTTCTTGAACTTCCTGTTCGTTCTGGTTTAATTTGGGCACGTTTAGCGGGTGCAAGAT
TGGCATCTGGTGATGTTTTAATATTTTTAGACTCACATACTGAAGCTAATACTAATTGGA
TGCCACCATTACTTGAACCAATTGCTAAAAATTATCGCATTTGTACTTGTCCATTTATTG
ATGTCATTGAGTTTACTAATTTTGAATATGTCATTCAGGATGAAGGATCGAGAGGTAAAT
TTGAACAAAAACAAAAAAACTAGAACTCAAGCCAGGCTTCCAAAAACGACCAACTGATCC
ATTTCCTTCTCCAATCATGGCTGGTGGACTTTTTGCAATTTCAGCAAAATTCTTTTGGGA
ACTTGGTGGATATGATCCAGGCTTAGATGTCTGGGGTGGTGAGCAGTATGAATTGAGCTT
CAAAATATGGCTTTGTGGTGGTGAGATGTATGACATTCCGTGTTCAAGAGTTGGACATAT
TTACAGAGGATCAATGCCATTTGAAGATGATAGAAAAGGAATTGACTTTCTTGCTATCAA
CTACAAACGAGTAGCAGAAGTTTGGTTAGGTGATGAATACAAAAATTATCTCTACATGCG
AGATCCAGAAAGATATGGTCGAGTTGATGCTGGTGATATTTCATATCAGCTTGCTATCAA
AAAGAAACTTCAATGCAAGCCATTTTCATATTTTCTCAATGAAGTTGCAAGTGACATGCT
TGAATATTATCCATTAATTGATCCACCACCATTTGCTTATGGTGTCATTCAAAGTATGCT
TAATCCAATGATTTGTATTGATACTTATGGAAAAGATGAAAAAAGTGAACTTGGACTTTA
TGGTTGTGCTCGTGATTTACAAAATCCACAAAAAACTCAATTTTTTACTCTTCGACATTT
TCGTGACATTGAATTGAAAGGAACAATGTTTTGTTTTGATCAAAATGAATTTGGTCAACT
AGTAACTGGCATATGTCATCATGCACAAGGAAATCAATATTTTAGATATGATTTAAGAAC
ACAACAAATTTATCATGCTGGTGAAGCACGAAATGAATGCATTGATATGGATCCAAGTAA
AAGTGATGAAGGTGCTGTCTTTTTTGCCCCATGTGATTCCGAATCTTTAACACAAAAGTG
GAAATTTGGATTTATTAATGAGACAGCTTTAAATAATTGGACAAAATATGGAGCAGAAAT
TCCAAATTTTGATGAACTAAAACGACTTGAAGGAATTTATCATTAG
>g17454.t2 Gene=g17454 Length=309
MAGGLFAISAKFFWELGGYDPGLDVWGGEQYELSFKIWLCGGEMYDIPCSRVGHIYRGSM
PFEDDRKGIDFLAINYKRVAEVWLGDEYKNYLYMRDPERYGRVDAGDISYQLAIKKKLQC
KPFSYFLNEVASDMLEYYPLIDPPPFAYGVIQSMLNPMICIDTYGKDEKSELGLYGCARD
LQNPQKTQFFTLRHFRDIELKGTMFCFDQNEFGQLVTGICHHAQGNQYFRYDLRTQQIYH
AGEARNECIDMDPSKSDEGAVFFAPCDSESLTQKWKFGFINETALNNWTKYGAEIPNFDE
LKRLEGIYH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g17454.t2 | CDD | cd00161 | RICIN | 149 | 277 | 0.000 |
| 8 | g17454.t2 | Gene3D | G3DSA:3.90.550.10 | Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A | 1 | 141 | 0.000 |
| 7 | g17454.t2 | Gene3D | G3DSA:2.80.10.50 | - | 145 | 283 | 0.000 |
| 2 | g17454.t2 | PANTHER | PTHR11675 | N-ACETYLGALACTOSAMINYLTRANSFERASE | 1 | 289 | 0.000 |
| 3 | g17454.t2 | PANTHER | PTHR11675:SF40 | POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE-LIKE 6 | 1 | 289 | 0.000 |
| 1 | g17454.t2 | Pfam | PF00652 | Ricin-type beta-trefoil lectin domain | 148 | 275 | 0.000 |
| 9 | g17454.t2 | ProSiteProfiles | PS50231 | Lectin domain of ricin B chain profile. | 206 | 277 | 12.483 |
| 6 | g17454.t2 | SMART | SM00458 | ricin_3 | 146 | 278 | 0.000 |
| 5 | g17454.t2 | SUPERFAMILY | SSF53448 | Nucleotide-diphospho-sugar transferases | 2 | 132 | 0.000 |
| 4 | g17454.t2 | SUPERFAMILY | SSF50370 | Ricin B-like lectins | 141 | 278 | 0.000 |
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.
