General information for g6549.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t6 | TTS | g6549.t6 | 17607414 | 17607414 |
| chr_2 | g6549 | g6549.t6 | isoform | g6549.t6 | 17607704 | 17610355 |
| chr_2 | g6549 | g6549.t6 | exon | g6549.t6.exon1 | 17607704 | 17607710 |
| chr_2 | g6549 | g6549.t6 | exon | g6549.t6.exon2 | 17608282 | 17608688 |
| chr_2 | g6549 | g6549.t6 | cds | g6549.t6.CDS1 | 17608515 | 17608688 |
| chr_2 | g6549 | g6549.t6 | exon | g6549.t6.exon3 | 17608761 | 17608929 |
| chr_2 | g6549 | g6549.t6 | cds | g6549.t6.CDS2 | 17608761 | 17608929 |
| chr_2 | g6549 | g6549.t6 | exon | g6549.t6.exon4 | 17609123 | 17609187 |
| chr_2 | g6549 | g6549.t6 | cds | g6549.t6.CDS3 | 17609123 | 17609187 |
| chr_2 | g6549 | g6549.t6 | exon | g6549.t6.exon5 | 17609254 | 17609393 |
| chr_2 | g6549 | g6549.t6 | cds | g6549.t6.CDS4 | 17609254 | 17609393 |
| chr_2 | g6549 | g6549.t6 | exon | g6549.t6.exon6 | 17610088 | 17610268 |
| chr_2 | g6549 | g6549.t6 | cds | g6549.t6.CDS5 | 17610088 | 17610268 |
| chr_2 | g6549 | g6549.t6 | exon | g6549.t6.exon7 | 17610327 | 17610355 |
| chr_2 | g6549 | g6549.t6 | cds | g6549.t6.CDS6 | 17610327 | 17610338 |
| chr_2 | g6549 | g6549.t6 | TSS | g6549.t6 | NA | NA |
Sequences
>g6549.t6 Gene=g6549 Length=998
GTGGTGAAAATTTGGAAATGAGTTTTCGTATTTGGCAATGCGGCGGAATTTTGGAAATTG
CTCCCTGTAGCCACGTTGGTCATGTTTTCAGAGATAAAAGTCCATATACTTTCCCTGGCG
GTGTGGCAAATATTGTACTTAAAAATGCTGCTCGTGTTGCAGCTGTTTGGCTTGACGAAT
GGAAAGAATTTTACTTCGCTATGAGTCCAGGTGCACGAAAAACATCAGCTGGAGATGTGT
CTGCACGTCTTGCTCTAAGAGAAAAATTAAAGTGCAAGAGTTTCAGATGGTATCTTGAAA
ATATTTATCCTGAGAGTCAAATGCCATTAGATTATTATTTCCTCGGAGAAATTCGAAATG
TCGAAAGTCAGAATTGTTTAGATACGATGGGTCATAAATCAGGAGAGAAAGTTGGATCAT
CATATTGTCACGGACTGGGAGGTAATCAAGTTTTCGCCTACACTAAACGACAACAAATTA
TGTCAGATGATAACTGTCTTGATGCCAGTAACGCTCATGGACCAGTTAACTTAGTTAGAT
GTCATGGAATGGGTGGGAATCAGGAATGGAGTTATGATGAGACTGACCTTACAATTAAGC
ATGTGAATTCAGGAAATTGTCTTACAAGAGCCACTCGAGAAGATCCTTCAACGCCACAAC
TTCGTCCATGTAACTTTTCTAAAGGTCAACAGTGGTTAATGCAATCAAAGTTTAAGTGGC
AAACAAAGCAAGGTACAGAAGATGAAGAGAGAAGATAGGGGTTGCTGAAATTGGCCAATA
TGGATTGATTTAATTTATTTTCCTACATCGTTCCTCTTATCTTGTACAATATAAGACCCC
ATTTTTATATAATTTCTTTTTGCAAGAAACATCCGGAACAAACTTAAACTAAGTTCTTTA
GATATACATAAACCAACAATGAACATGCGATTTCCATTTTAGACAATCAGTTATTTTCGA
TAAAATACAAACCACTTAGATAGATTACAAAAAGAGAT
>g6549.t6 Gene=g6549 Length=246
MSFRIWQCGGILEIAPCSHVGHVFRDKSPYTFPGGVANIVLKNAARVAAVWLDEWKEFYF
AMSPGARKTSAGDVSARLALREKLKCKSFRWYLENIYPESQMPLDYYFLGEIRNVESQNC
LDTMGHKSGEKVGSSYCHGLGGNQVFAYTKRQQIMSDDNCLDASNAHGPVNLVRCHGMGG
NQEWSYDETDLTIKHVNSGNCLTRATREDPSTPQLRPCNFSKGQQWLMQSKFKWQTKQGT
EDEERR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g6549.t6 | CDD | cd00161 | RICIN | 110 | 228 | 0.000 |
| 8 | g6549.t6 | Gene3D | G3DSA:3.90.550.10 | Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A | 1 | 99 | 0.000 |
| 7 | g6549.t6 | Gene3D | G3DSA:2.80.10.50 | - | 105 | 233 | 0.000 |
| 2 | g6549.t6 | PANTHER | PTHR11675 | N-ACETYLGALACTOSAMINYLTRANSFERASE | 1 | 230 | 0.000 |
| 3 | g6549.t6 | PANTHER | PTHR11675:SF47 | POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 13 | 1 | 230 | 0.000 |
| 1 | g6549.t6 | Pfam | PF00652 | Ricin-type beta-trefoil lectin domain | 109 | 226 | 0.000 |
| 9 | g6549.t6 | ProSiteProfiles | PS50231 | Lectin domain of ricin B chain profile. | 120 | 229 | 21.076 |
| 6 | g6549.t6 | SMART | SM00458 | ricin_3 | 106 | 229 | 0.000 |
| 5 | g6549.t6 | SUPERFAMILY | SSF53448 | Nucleotide-diphospho-sugar transferases | 1 | 99 | 0.000 |
| 4 | g6549.t6 | SUPERFAMILY | SSF50370 | Ricin B-like lectins | 102 | 229 | 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.
