Gene loci information

Transcript annotation

  • This transcript has been annotated as Polypeptide N-acetylgalactosaminyltransferase 5.

Parent gene

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.t8 TTS g6549.t8 17607799 17607799
chr_2 g6549 g6549.t8 isoform g6549.t8 17608515 17610355
chr_2 g6549 g6549.t8 exon g6549.t8.exon1 17608515 17608688
chr_2 g6549 g6549.t8 cds g6549.t8.CDS1 17608515 17608688
chr_2 g6549 g6549.t8 exon g6549.t8.exon2 17608761 17608929
chr_2 g6549 g6549.t8 cds g6549.t8.CDS2 17608761 17608929
chr_2 g6549 g6549.t8 exon g6549.t8.exon3 17609123 17609187
chr_2 g6549 g6549.t8 cds g6549.t8.CDS3 17609123 17609187
chr_2 g6549 g6549.t8 exon g6549.t8.exon4 17609254 17609393
chr_2 g6549 g6549.t8 cds g6549.t8.CDS4 17609254 17609393
chr_2 g6549 g6549.t8 exon g6549.t8.exon5 17610088 17610268
chr_2 g6549 g6549.t8 cds g6549.t8.CDS5 17610088 17610097
chr_2 g6549 g6549.t8 exon g6549.t8.exon6 17610323 17610355
chr_2 g6549 g6549.t8 TSS g6549.t8 NA NA

Sequences

>g6549.t8 Gene=g6549 Length=762
GTGGTGAAAATTTGGAAATGAGTTTTCGTGTAAATTTGGCAATGCGGCGGAATTTTGGAA
ATTGCTCCCTGTAGCCACGTTGGTCATGTTTTCAGAGATAAAAGTCCATATACTTTCCCT
GGCGGTGTGGCAAATATTGTACTTAAAAATGCTGCTCGTGTTGCAGCTGTTTGGCTTGAC
GAATGGAAAGAATTTTACTTCGCTATGAGTCCAGGTGCACGAAAAACATCAGCTGGAGAT
GTGTCTGCACGTCTTGCTCTAAGAGAAAAATTAAAGTGCAAGAGTTTCAGATGGTATCTT
GAAAATATTTATCCTGAGAGTCAAATGCCATTAGATTATTATTTCCTCGGAGAAATTCGA
AATGTCGAAAGTCAGAATTGTTTAGATACGATGGGTCATAAATCAGGAGAGAAAGTTGGA
TCATCATATTGTCACGGACTGGGAGGTAATCAAGTTTTCGCCTACACTAAACGACAACAA
ATTATGTCAGATGATAACTGTCTTGATGCCAGTAACGCTCATGGACCAGTTAACTTAGTT
AGATGTCATGGAATGGGTGGGAATCAGGAATGGAGTTATGATGAGACTGACCTTACAATT
AAGCATGTGAATTCAGGAAATTGTCTTACAAGAGCCACTCGAGAAGATCCTTCAACGCCA
CAACTTCGTCCATGTAACTTTTCTAAAGGTCAACAGTGGTTAATGCAATCAAAGTTTAAG
TGGCAAACAAAGCAAGGTACAGAAGATGAAGAGAGAAGATAG

>g6549.t8 Gene=g6549 Length=185
MSPGARKTSAGDVSARLALREKLKCKSFRWYLENIYPESQMPLDYYFLGEIRNVESQNCL
DTMGHKSGEKVGSSYCHGLGGNQVFAYTKRQQIMSDDNCLDASNAHGPVNLVRCHGMGGN
QEWSYDETDLTIKHVNSGNCLTRATREDPSTPQLRPCNFSKGQQWLMQSKFKWQTKQGTE
DEERR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g6549.t8 CDD cd00161 RICIN 49 167 0.000
7 g6549.t8 Gene3D G3DSA:1.10.8.460 - 1 42 0.000
6 g6549.t8 Gene3D G3DSA:2.80.10.50 - 44 172 0.000
2 g6549.t8 PANTHER PTHR11675 N-ACETYLGALACTOSAMINYLTRANSFERASE 1 169 0.000
3 g6549.t8 PANTHER PTHR11675:SF47 POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 13 1 169 0.000
1 g6549.t8 Pfam PF00652 Ricin-type beta-trefoil lectin domain 48 165 0.000
8 g6549.t8 ProSiteProfiles PS50231 Lectin domain of ricin B chain profile. 59 168 21.076
5 g6549.t8 SMART SM00458 ricin_3 45 168 0.000
4 g6549.t8 SUPERFAMILY SSF50370 Ricin B-like lectins 41 168 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. There were no conditions that were differentially expressed