General information for g6549.t17
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.t17 | isoform | g6549.t17 | 17610100 | 17613764 |
| chr_2 | g6549 | g6549.t17 | exon | g6549.t17.exon1 | 17610100 | 17610268 |
| chr_2 | g6549 | g6549.t17 | cds | g6549.t17.CDS1 | 17610101 | 17610268 |
| chr_2 | g6549 | g6549.t17 | exon | g6549.t17.exon2 | 17610327 | 17610355 |
| chr_2 | g6549 | g6549.t17 | cds | g6549.t17.CDS2 | 17610327 | 17610355 |
| chr_2 | g6549 | g6549.t17 | exon | g6549.t17.exon3 | 17610418 | 17610493 |
| chr_2 | g6549 | g6549.t17 | cds | g6549.t17.CDS3 | 17610418 | 17610493 |
| chr_2 | g6549 | g6549.t17 | exon | g6549.t17.exon4 | 17610549 | 17610782 |
| chr_2 | g6549 | g6549.t17 | cds | g6549.t17.CDS4 | 17610549 | 17610782 |
| chr_2 | g6549 | g6549.t17 | exon | g6549.t17.exon5 | 17610849 | 17610949 |
| chr_2 | g6549 | g6549.t17 | cds | g6549.t17.CDS5 | 17610849 | 17610949 |
| chr_2 | g6549 | g6549.t17 | exon | g6549.t17.exon6 | 17611007 | 17611230 |
| chr_2 | g6549 | g6549.t17 | cds | g6549.t17.CDS6 | 17611007 | 17611230 |
| chr_2 | g6549 | g6549.t17 | exon | g6549.t17.exon7 | 17611334 | 17611677 |
| chr_2 | g6549 | g6549.t17 | cds | g6549.t17.CDS7 | 17611334 | 17611677 |
| chr_2 | g6549 | g6549.t17 | exon | g6549.t17.exon8 | 17612615 | 17612835 |
| chr_2 | g6549 | g6549.t17 | cds | g6549.t17.CDS8 | 17612615 | 17612671 |
| chr_2 | g6549 | g6549.t17 | exon | g6549.t17.exon9 | 17613757 | 17613764 |
| chr_2 | g6549 | g6549.t17 | TSS | g6549.t17 | 17613807 | 17613807 |
| chr_2 | g6549 | g6549.t17 | TTS | g6549.t17 | NA | NA |
Sequences
>g6549.t17 Gene=g6549 Length=1406
ATTAAAAAAAGTTTGAATGAAAACACAAAAAATTTCGTACATCAATCTGCACCATCAACC
AAACTCAATGTCTAATTATTCGAGAATGTTTCGTGGACGTATACGTACGAGTACTTGTAG
AATTATTCTAATAACTTCTTTAGCATGGCTTCTAATAGACGTGATCATAATTATGAAATA
CACTGATGGTCTCAATGGCGGATTATTTAAAAAATCTAGAGATAATGAGGTTCATGAAGA
TAAATTTATCAGTCACCATCAACTTGACGAAGATCCAATTGTTAACGATGATGAAATAAA
TACAAATTTAAATAATGCTGATAATGATTTTAACAATGATGATGACGTGATACACATATC
GAAAACATATCGATCGACAGATCTAAAGAAATGGCGGCCAGCGCCGGTGGTGCGTGAAAA
TGTAGGAAAACCAGGTGAAATGGGCAAGCCGGTCAAAATGAAATCATATCAGCAGGAAGA
AATGAAAGAGAAATTCAAAGAAAATCAATTCAATTTGTTAGCAAGTGATATGATATGGTT
GAATCGATCGCTCGCTGATGTGCGGCACAAAGACTGTCGAACTAAAACATACCCAAGTAG
ATTGCCAACAACAAGTATAGTTATAGTTTTTCATAATGAAGCATGGAGCACATTGCTCAG
AACAATATGGAGTGTAATTAATCGTTCACCACGACCGTTATTAAAAGAAATCATTCTCGT
TGATGATGCAAGCGAGCGTGAATATTTAGGTGAAAAATTAGAGGAATATGTAAAAACACT
GCCTGTTCCAACATCAGTTTTACGCACCGGTAAAAGGTCTGGTCTCATTAGAGCACGTTT
ATTGGGTGCTGCTGCTGTAAAAGGTCAAGTTATAACTTTTCTCGATGCTCATTGTGAATG
TACTGAAGGTTGGTTAGAACCTTTGTTGTCGAGAATTGCTTTGGACAGAAAAACAGTTGT
TTGTCCAATAATCGATGTTATTAGTGATGAAACGTTTGAATATGTTACTGCTTCTGATCA
AACTTGGGGTGGTTTTAATTGGAAGCTCAATTTTAGATGGTATCGAGTACCTGCTAGAGA
AATGGCAAGAAGAAATAATGATAGGACTTCACCTCTTCGAACGCCAACTATGGCGGGTGG
TTTGTTTTCAATAGATAAAGATTATTTCTATGAAATTGGTTCATATGACGAGGGAATGGA
TATTTGGGGTGGTGAAAATTTGGAAATGAGTTTTCGTATTTGGCAATGCGGCGGAATTTT
GGAAATTGCTCCCTGTAGCCACGTTGGTCATGTTTTCAGAGATAAAAGTCCATATACTTT
CCCTGGCGGTGTGGCAAATATTGTACTTAAAAATGCTGCTCGTGTTGCAGCTGTTTGGCT
TGACGAATGGAAAGAATTTTACTTCG
>g6549.t17 Gene=g6549 Length=411
MKYTDGLNGGLFKKSRDNEVHEDKFISHHQLDEDPIVNDDEINTNLNNADNDFNNDDDVI
HISKTYRSTDLKKWRPAPVVRENVGKPGEMGKPVKMKSYQQEEMKEKFKENQFNLLASDM
IWLNRSLADVRHKDCRTKTYPSRLPTTSIVIVFHNEAWSTLLRTIWSVINRSPRPLLKEI
ILVDDASEREYLGEKLEEYVKTLPVPTSVLRTGKRSGLIRARLLGAAAVKGQVITFLDAH
CECTEGWLEPLLSRIALDRKTVVCPIIDVISDETFEYVTASDQTWGGFNWKLNFRWYRVP
AREMARRNNDRTSPLRTPTMAGGLFSIDKDYFYEIGSYDEGMDIWGGENLEMSFRIWQCG
GILEIAPCSHVGHVFRDKSPYTFPGGVANIVLKNAARVAAVWLDEWKEFYF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g6549.t17 | CDD | cd02510 | pp-GalNAc-T | 148 | 411 | 0 |
| 5 | g6549.t17 | Gene3D | G3DSA:3.90.550.10 | Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A | 69 | 411 | 0 |
| 2 | g6549.t17 | PANTHER | PTHR11675 | N-ACETYLGALACTOSAMINYLTRANSFERASE | 70 | 411 | 0 |
| 3 | g6549.t17 | PANTHER | PTHR11675:SF101 | POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 1 | 70 | 411 | 0 |
| 1 | g6549.t17 | Pfam | PF00535 | Glycosyl transferase family 2 | 148 | 332 | 0 |
| 4 | g6549.t17 | SUPERFAMILY | SSF53448 | Nucleotide-diphospho-sugar transferases | 124 | 410 | 0 |
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. There were no conditions that were differentially expressed