General information for g6549.t18
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.t18 | isoform | g6549.t18 | 17610554 | 17613764 |
| chr_2 | g6549 | g6549.t18 | exon | g6549.t18.exon1 | 17610554 | 17610782 |
| chr_2 | g6549 | g6549.t18 | cds | g6549.t18.CDS1 | 17610555 | 17610782 |
| chr_2 | g6549 | g6549.t18 | exon | g6549.t18.exon2 | 17610849 | 17610949 |
| chr_2 | g6549 | g6549.t18 | cds | g6549.t18.CDS2 | 17610849 | 17610949 |
| chr_2 | g6549 | g6549.t18 | exon | g6549.t18.exon3 | 17611007 | 17611230 |
| chr_2 | g6549 | g6549.t18 | cds | g6549.t18.CDS3 | 17611007 | 17611230 |
| chr_2 | g6549 | g6549.t18 | exon | g6549.t18.exon4 | 17611334 | 17611677 |
| chr_2 | g6549 | g6549.t18 | cds | g6549.t18.CDS4 | 17611334 | 17611677 |
| chr_2 | g6549 | g6549.t18 | exon | g6549.t18.exon5 | 17612615 | 17612835 |
| chr_2 | g6549 | g6549.t18 | cds | g6549.t18.CDS5 | 17612615 | 17612671 |
| chr_2 | g6549 | g6549.t18 | exon | g6549.t18.exon6 | 17613757 | 17613764 |
| chr_2 | g6549 | g6549.t18 | TSS | g6549.t18 | 17613807 | 17613807 |
| chr_2 | g6549 | g6549.t18 | TTS | g6549.t18 | NA | NA |
Sequences
>g6549.t18 Gene=g6549 Length=1127
ATTAAAAAAAGTTTGAATGAAAACACAAAAAATTTCGTACATCAATCTGCACCATCAACC
AAACTCAATGTCTAATTATTCGAGAATGTTTCGTGGACGTATACGTACGAGTACTTGTAG
AATTATTCTAATAACTTCTTTAGCATGGCTTCTAATAGACGTGATCATAATTATGAAATA
CACTGATGGTCTCAATGGCGGATTATTTAAAAAATCTAGAGATAATGAGGTTCATGAAGA
TAAATTTATCAGTCACCATCAACTTGACGAAGATCCAATTGTTAACGATGATGAAATAAA
TACAAATTTAAATAATGCTGATAATGATTTTAACAATGATGATGACGTGATACACATATC
GAAAACATATCGATCGACAGATCTAAAGAAATGGCGGCCAGCGCCGGTGGTGCGTGAAAA
TGTAGGAAAACCAGGTGAAATGGGCAAGCCGGTCAAAATGAAATCATATCAGCAGGAAGA
AATGAAAGAGAAATTCAAAGAAAATCAATTCAATTTGTTAGCAAGTGATATGATATGGTT
GAATCGATCGCTCGCTGATGTGCGGCACAAAGACTGTCGAACTAAAACATACCCAAGTAG
ATTGCCAACAACAAGTATAGTTATAGTTTTTCATAATGAAGCATGGAGCACATTGCTCAG
AACAATATGGAGTGTAATTAATCGTTCACCACGACCGTTATTAAAAGAAATCATTCTCGT
TGATGATGCAAGCGAGCGTGAATATTTAGGTGAAAAATTAGAGGAATATGTAAAAACACT
GCCTGTTCCAACATCAGTTTTACGCACCGGTAAAAGGTCTGGTCTCATTAGAGCACGTTT
ATTGGGTGCTGCTGCTGTAAAAGGTCAAGTTATAACTTTTCTCGATGCTCATTGTGAATG
TACTGAAGGTTGGTTAGAACCTTTGTTGTCGAGAATTGCTTTGGACAGAAAAACAGTTGT
TTGTCCAATAATCGATGTTATTAGTGATGAAACGTTTGAATATGTTACTGCTTCTGATCA
AACTTGGGGTGGTTTTAATTGGAAGCTCAATTTTAGATGGTATCGAGTACCTGCTAGAGA
AATGGCAAGAAGAAATAATGATAGGACTTCACCTCTTCGAACGCCAA
>g6549.t18 Gene=g6549 Length=318
MKYTDGLNGGLFKKSRDNEVHEDKFISHHQLDEDPIVNDDEINTNLNNADNDFNNDDDVI
HISKTYRSTDLKKWRPAPVVRENVGKPGEMGKPVKMKSYQQEEMKEKFKENQFNLLASDM
IWLNRSLADVRHKDCRTKTYPSRLPTTSIVIVFHNEAWSTLLRTIWSVINRSPRPLLKEI
ILVDDASEREYLGEKLEEYVKTLPVPTSVLRTGKRSGLIRARLLGAAAVKGQVITFLDAH
CECTEGWLEPLLSRIALDRKTVVCPIIDVISDETFEYVTASDQTWGGFNWKLNFRWYRVP
AREMARRNNDRTSPLRTP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g6549.t18 | Gene3D | G3DSA:3.90.550.10 | Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A | 68 | 318 | 0 |
| 2 | g6549.t18 | PANTHER | PTHR11675 | N-ACETYLGALACTOSAMINYLTRANSFERASE | 70 | 318 | 0 |
| 3 | g6549.t18 | PANTHER | PTHR11675:SF101 | POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 1 | 70 | 318 | 0 |
| 1 | g6549.t18 | Pfam | PF00535 | Glycosyl transferase family 2 | 148 | 287 | 0 |
| 4 | g6549.t18 | SUPERFAMILY | SSF53448 | Nucleotide-diphospho-sugar transferases | 124 | 317 | 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 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.
