General information for g6549.t1
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.t1 | TTS | g6549.t1 | 17607799 | 17607799 |
| chr_2 | g6549 | g6549.t1 | isoform | g6549.t1 | 17608515 | 17612758 |
| chr_2 | g6549 | g6549.t1 | exon | g6549.t1.exon1 | 17608515 | 17608688 |
| chr_2 | g6549 | g6549.t1 | cds | g6549.t1.CDS1 | 17608515 | 17608688 |
| chr_2 | g6549 | g6549.t1 | exon | g6549.t1.exon2 | 17608761 | 17608929 |
| chr_2 | g6549 | g6549.t1 | cds | g6549.t1.CDS2 | 17608761 | 17608929 |
| chr_2 | g6549 | g6549.t1 | exon | g6549.t1.exon3 | 17609123 | 17609187 |
| chr_2 | g6549 | g6549.t1 | cds | g6549.t1.CDS3 | 17609123 | 17609187 |
| chr_2 | g6549 | g6549.t1 | exon | g6549.t1.exon4 | 17609254 | 17609393 |
| chr_2 | g6549 | g6549.t1 | cds | g6549.t1.CDS4 | 17609254 | 17609393 |
| chr_2 | g6549 | g6549.t1 | exon | g6549.t1.exon5 | 17610088 | 17610268 |
| chr_2 | g6549 | g6549.t1 | cds | g6549.t1.CDS5 | 17610088 | 17610268 |
| chr_2 | g6549 | g6549.t1 | exon | g6549.t1.exon6 | 17610327 | 17610355 |
| chr_2 | g6549 | g6549.t1 | cds | g6549.t1.CDS6 | 17610327 | 17610355 |
| chr_2 | g6549 | g6549.t1 | exon | g6549.t1.exon7 | 17610418 | 17610493 |
| chr_2 | g6549 | g6549.t1 | cds | g6549.t1.CDS7 | 17610418 | 17610493 |
| chr_2 | g6549 | g6549.t1 | exon | g6549.t1.exon8 | 17610549 | 17610782 |
| chr_2 | g6549 | g6549.t1 | cds | g6549.t1.CDS8 | 17610549 | 17610782 |
| chr_2 | g6549 | g6549.t1 | exon | g6549.t1.exon9 | 17610849 | 17610949 |
| chr_2 | g6549 | g6549.t1 | cds | g6549.t1.CDS9 | 17610849 | 17610949 |
| chr_2 | g6549 | g6549.t1 | exon | g6549.t1.exon10 | 17611007 | 17611230 |
| chr_2 | g6549 | g6549.t1 | cds | g6549.t1.CDS10 | 17611007 | 17611230 |
| chr_2 | g6549 | g6549.t1 | exon | g6549.t1.exon11 | 17611334 | 17611677 |
| chr_2 | g6549 | g6549.t1 | cds | g6549.t1.CDS11 | 17611334 | 17611677 |
| chr_2 | g6549 | g6549.t1 | exon | g6549.t1.exon12 | 17612615 | 17612758 |
| chr_2 | g6549 | g6549.t1 | cds | g6549.t1.CDS12 | 17612615 | 17612671 |
| chr_2 | g6549 | g6549.t1 | TSS | g6549.t1 | NA | NA |
Sequences
>g6549.t1 Gene=g6549 Length=1881
ATGTTTCGTGGACGTATACGTACGAGTACTTGTAGAATTATTCTAATAACTTCTTTAGCA
TGGCTTCTAATAGACGTGATCATAATTATGAAATACACTGATGGTCTCAATGGCGGATTA
TTTAAAAAATCTAGAGATAATGAGGTTCATGAAGATAAATTTATCAGTCACCATCAACTT
GACGAAGATCCAATTGTTAACGATGATGAAATAAATACAAATTTAAATAATGCTGATAAT
GATTTTAACAATGATGATGACGTGATACACATATCGAAAACATATCGATCGACAGATCTA
AAGAAATGGCGGCCAGCGCCGGTGGTGCGTGAAAATGTAGGAAAACCAGGTGAAATGGGC
AAGCCGGTCAAAATGAAATCATATCAGCAGGAAGAAATGAAAGAGAAATTCAAAGAAAAT
CAATTCAATTTGTTAGCAAGTGATATGATATGGTTGAATCGATCGCTCGCTGATGTGCGG
CACAAAGACTGTCGAACTAAAACATACCCAAGTAGATTGCCAACAACAAGTATAGTTATA
GTTTTTCATAATGAAGCATGGAGCACATTGCTCAGAACAATATGGAGTGTAATTAATCGT
TCACCACGACCGTTATTAAAAGAAATCATTCTCGTTGATGATGCAAGCGAGCGTGAATAT
TTAGGTGAAAAATTAGAGGAATATGTAAAAACACTGCCTGTTCCAACATCAGTTTTACGC
ACCGGTAAAAGGTCTGGTCTCATTAGAGCACGTTTATTGGGTGCTGCTGCTGTAAAAGGT
CAAGTTATAACTTTTCTCGATGCTCATTGTGAATGTACTGAAGGTTGGTTAGAACCTTTG
TTGTCGAGAATTGCTTTGGACAGAAAAACAGTTGTTTGTCCAATAATCGATGTTATTAGT
GATGAAACGTTTGAATATGTTACTGCTTCTGATCAAACTTGGGGTGGTTTTAATTGGAAG
CTCAATTTTAGATGGTATCGAGTACCTGCTAGAGAAATGGCAAGAAGAAATAATGATAGG
ACTTCACCTCTTCGAACGCCAACTATGGCGGGTGGTTTGTTTTCAATAGATAAAGATTAT
TTCTATGAAATTGGTTCATATGACGAGGGAATGGATATTTGGGGTGGTGAAAATTTGGAA
ATGAGTTTTCGTATTTGGCAATGCGGCGGAATTTTGGAAATTGCTCCCTGTAGCCACGTT
GGTCATGTTTTCAGAGATAAAAGTCCATATACTTTCCCTGGCGGTGTGGCAAATATTGTA
CTTAAAAATGCTGCTCGTGTTGCAGCTGTTTGGCTTGACGAATGGAAAGAATTTTACTTC
GCTATGAGTCCAGGTGCACGAAAAACATCAGCTGGAGATGTGTCTGCACGTCTTGCTCTA
AGAGAAAAATTAAAGTGCAAGAGTTTCAGATGGTATCTTGAAAATATTTATCCTGAGAGT
CAAATGCCATTAGATTATTATTTCCTCGGAGAAATTCGAAATGTCGAAAGTCAGAATTGT
TTAGATACGATGGGTCATAAATCAGGAGAGAAAGTTGGATCATCATATTGTCACGGACTG
GGAGGTAATCAAGTTTTCGCCTACACTAAACGACAACAAATTATGTCAGATGATAACTGT
CTTGATGCCAGTAACGCTCATGGACCAGTTAACTTAGTTAGATGTCATGGAATGGGTGGG
AATCAGGAATGGAGTTATGATGAGACTGACCTTACAATTAAGCATGTGAATTCAGGAAAT
TGTCTTACAAGAGCCACTCGAGAAGATCCTTCAACGCCACAACTTCGTCCATGTAACTTT
TCTAAAGGTCAACAGTGGTTAATGCAATCAAAGTTTAAGTGGCAAACAAAGCAAGGTACA
GAAGATGAAGAGAGAAGATAG
>g6549.t1 Gene=g6549 Length=597
MKYTDGLNGGLFKKSRDNEVHEDKFISHHQLDEDPIVNDDEINTNLNNADNDFNNDDDVI
HISKTYRSTDLKKWRPAPVVRENVGKPGEMGKPVKMKSYQQEEMKEKFKENQFNLLASDM
IWLNRSLADVRHKDCRTKTYPSRLPTTSIVIVFHNEAWSTLLRTIWSVINRSPRPLLKEI
ILVDDASEREYLGEKLEEYVKTLPVPTSVLRTGKRSGLIRARLLGAAAVKGQVITFLDAH
CECTEGWLEPLLSRIALDRKTVVCPIIDVISDETFEYVTASDQTWGGFNWKLNFRWYRVP
AREMARRNNDRTSPLRTPTMAGGLFSIDKDYFYEIGSYDEGMDIWGGENLEMSFRIWQCG
GILEIAPCSHVGHVFRDKSPYTFPGGVANIVLKNAARVAAVWLDEWKEFYFAMSPGARKT
SAGDVSARLALREKLKCKSFRWYLENIYPESQMPLDYYFLGEIRNVESQNCLDTMGHKSG
EKVGSSYCHGLGGNQVFAYTKRQQIMSDDNCLDASNAHGPVNLVRCHGMGGNQEWSYDET
DLTIKHVNSGNCLTRATREDPSTPQLRPCNFSKGQQWLMQSKFKWQTKQGTEDEERR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g6549.t1 | CDD | cd02510 | pp-GalNAc-T | 148 | 448 | 0.000 |
| 11 | g6549.t1 | CDD | cd00161 | RICIN | 461 | 579 | 0.000 |
| 9 | g6549.t1 | Gene3D | G3DSA:3.90.550.10 | Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A | 69 | 456 | 0.000 |
| 8 | g6549.t1 | Gene3D | G3DSA:2.80.10.50 | - | 457 | 584 | 0.000 |
| 3 | g6549.t1 | PANTHER | PTHR11675 | N-ACETYLGALACTOSAMINYLTRANSFERASE | 79 | 581 | 0.000 |
| 4 | g6549.t1 | PANTHER | PTHR11675:SF47 | POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 13 | 79 | 581 | 0.000 |
| 2 | g6549.t1 | Pfam | PF00535 | Glycosyl transferase family 2 | 148 | 332 | 0.000 |
| 1 | g6549.t1 | Pfam | PF00652 | Ricin-type beta-trefoil lectin domain | 460 | 577 | 0.000 |
| 10 | g6549.t1 | ProSiteProfiles | PS50231 | Lectin domain of ricin B chain profile. | 471 | 580 | 21.076 |
| 7 | g6549.t1 | SMART | SM00458 | ricin_3 | 457 | 580 | 0.000 |
| 6 | g6549.t1 | SUPERFAMILY | SSF53448 | Nucleotide-diphospho-sugar transferases | 124 | 450 | 0.000 |
| 5 | g6549.t1 | SUPERFAMILY | SSF50370 | Ricin B-like lectins | 453 | 580 | 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 transcript has been annotated with K00710 (polypeptide N-acetylgalactosaminyltransferase)
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.
