General information for g6549.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Polypeptide N-acetylgalactosaminyltransferase 5.
Parent gene
- The parent gene g6549 is located on chr_2: 17612608..17613894 (- 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_2 | g6549 | g6549.t4 | TTS | g6549.t4 | 17606620 | 17606620 |
| chr_2 | g6549 | g6549.t4 | isoform | g6549.t4 | 17607361 | 17609180 |
| chr_2 | g6549 | g6549.t4 | exon | g6549.t4.exon1 | 17607361 | 17608688 |
| chr_2 | g6549 | g6549.t4 | cds | g6549.t4.CDS1 | 17608515 | 17608688 |
| chr_2 | g6549 | g6549.t4 | exon | g6549.t4.exon2 | 17608761 | 17608929 |
| chr_2 | g6549 | g6549.t4 | cds | g6549.t4.CDS2 | 17608761 | 17608929 |
| chr_2 | g6549 | g6549.t4 | exon | g6549.t4.exon3 | 17609123 | 17609180 |
| chr_2 | g6549 | g6549.t4 | cds | g6549.t4.CDS3 | 17609123 | 17609151 |
| chr_2 | g6549 | g6549.t4 | TSS | g6549.t4 | NA | NA |
Sequences
>g6549.t4 Gene=g6549 Length=1555
ATGTCGAAAGTCAGAATTGTTTAGATACGATGGGTCATAAATCAGGAGAGAAAGTTGGAT
CATCATATTGTCACGGACTGGGAGGTAATCAAGTTTTCGCCTACACTAAACGACAACAAA
TTATGTCAGATGATAACTGTCTTGATGCCAGTAACGCTCATGGACCAGTTAACTTAGTTA
GATGTCATGGAATGGGTGGGAATCAGGAATGGAGTTATGATGAGACTGACCTTACAATTA
AGCATGTGAATTCAGGAAATTGTCTTACAAGAGCCACTCGAGAAGATCCTTCAACGCCAC
AACTTCGTCCATGTAACTTTTCTAAAGGTCAACAGTGGTTAATGCAATCAAAGTTTAAGT
GGCAAACAAAGCAAGGTACAGAAGATGAAGAGAGAAGATAGGGGTTGCTGAAATTGGCCA
ATATGGATTGATTTAATTTATTTTCCTACATCGTTCCTCTTATCTTGTACAATATAAGAC
CCCATTTTTATATAATTTCTTTTTGCAAGAAACATCCGGAACAAACTTAAACTAAGTTCT
TTAGATATACATAAACCAACAATGAACATGCGATTTCCATTTTAGACAATCAGTTATTTT
CGATAAAATACAAACCACTTAGATAGATTACAAAACAAAAGAAGAACAAGTATGAAGTAA
AAATTAAAATAATTAAGAAAGTTAGCAAAAGAATTAAATCTTTTGCAAAAAAAATAATGT
GATCAACCTATAATATGATGATTAAGTTGAAAAGAAAGGACCTTTTTGCAACACATTGTT
TAGTTCATTATTATTAATTGCGTTTAATACCTCGATGGATTTAGAGCATTTTTATTAGAG
AGTATATATAAAATTGAAATTTGCATATCACAATGCAAGGCACAACATAAATATTAGAAT
GGAACAATTTTTTCTAAGAAAAAAAATAGAGAGAGCCAGAATAATTGAGGATGTGTGTTT
CAAAAGCCAGAAAATGGAGATAAAAAATTTATATTAAGTATATATGTTGAAATTCATCGG
ATTCATGTGTTTAGAAATTAAGTAGGAATCAATTTATAAAATATTTAAAATCCTTTTTAT
ATTAACGTACTGCATTGTGTGCCACGAAGATTTTGGCAAAATAAAAAAAAAATGAATTAG
AAGAAAGAAATTAAAATCTCAATCTTCCGCAAGAACACACATTTCAAAATGATTTATATT
ACAAAAAGAGATGTATGTAAATAGAACAAATTTTGAGTAATCAGTTGATACAATTAAACA
CATGGTGGAGGTGCAATTTTCTTTACTCCCACAACTATCTTTAACAAAAATATCTCTCGT
TTATAAAATATTATTTAATGAAGAAAATAGAGTAACGTTATCAAAAATAATAGTATTTAG
TCGAATAAGATGTTATTTTCAATTTTTTTCGCCATTAAATTATTTTTTAATGAAAATCTT
TTCCTCTTTATATTTTTTTTCTTTTGTCTAAATGAATTTTAAATAAAGAGTATTTAATTA
TGAAATTTAATTGTGTTCATTCATTCCTGAAAATTGATAATTTGGCACTTTTAGA
>g6549.t4 Gene=g6549 Length=123
MGHKSGEKVGSSYCHGLGGNQVFAYTKRQQIMSDDNCLDASNAHGPVNLVRCHGMGGNQE
WSYDETDLTIKHVNSGNCLTRATREDPSTPQLRPCNFSKGQQWLMQSKFKWQTKQGTEDE
ERR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g6549.t4 | CDD | cd00161 | RICIN | 1 | 105 | 0.000 |
| 6 | g6549.t4 | Gene3D | G3DSA:2.80.10.50 | - | 1 | 110 | 0.000 |
| 2 | g6549.t4 | PANTHER | PTHR11675 | N-ACETYLGALACTOSAMINYLTRANSFERASE | 1 | 107 | 0.000 |
| 3 | g6549.t4 | PANTHER | PTHR11675:SF47 | POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 13 | 1 | 107 | 0.000 |
| 1 | g6549.t4 | Pfam | PF00652 | Ricin-type beta-trefoil lectin domain | 2 | 103 | 0.000 |
| 7 | g6549.t4 | ProSiteProfiles | PS50231 | Lectin domain of ricin B chain profile. | 1 | 106 | 18.042 |
| 5 | g6549.t4 | SMART | SM00458 | ricin_3 | 2 | 106 | 0.000 |
| 4 | g6549.t4 | SUPERFAMILY | SSF50370 | Ricin B-like lectins | 1 | 106 | 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.
