Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative polypeptide N-acetylgalactosaminyltransferase 9.

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_3 g2198 g2198.t2 isoform g2198.t2 15937728 15940100
chr_3 g2198 g2198.t2 exon g2198.t2.exon1 15937728 15937879
chr_3 g2198 g2198.t2 cds g2198.t2.CDS1 15937736 15937879
chr_3 g2198 g2198.t2 exon g2198.t2.exon2 15937940 15937972
chr_3 g2198 g2198.t2 cds g2198.t2.CDS2 15937940 15937972
chr_3 g2198 g2198.t2 exon g2198.t2.exon3 15939157 15939264
chr_3 g2198 g2198.t2 cds g2198.t2.CDS3 15939157 15939264
chr_3 g2198 g2198.t2 exon g2198.t2.exon4 15939325 15940100
chr_3 g2198 g2198.t2 cds g2198.t2.CDS4 15939325 15939486
chr_3 g2198 g2198.t2 TTS g2198.t2 15940899 15940899
chr_3 g2198 g2198.t2 TSS g2198.t2 NA NA

Sequences

>g2198.t2 Gene=g2198 Length=1069
AGGTATGGATGGATGATTACTCGAAATATTATTATCAAAGAATTGGATCAGATAAGGGTG
ATTTTGGTGATATCAGCTCTAGAGTTCAACTTAGAAAGGATTTAAAATGTAAAAGCTTCC
AATGGTATCTCGACACAATCTTCCCAGAATTGTTTATACCAGGTGATGCAGTGGCACAAG
GAGAGTATTGGATGCTCTCAAAAACTGGAGAGATTCGCAGAGACGAAGCATGTTTGGATT
ATGCTGGCTCTGATGTTATTCTTTATCCATGCCATGGTGGTAAAGGCAATCAGTTCTGGA
ATTATCGATTTGACACAAAGCAACTTCATCACAAATCATCAGATAGATGTATGGAAATCA
GTAGTGATCATCAGAAACTATTGATGGTTGAATGCAATTCACATCGTGATGCACAAAAAT
GGTACTTTGAAAATTACGACCCAAGCAAACTGTAAAAAGAAACAGGAAAATTCCTATCGC
AATAAAAACAATATTTTTGATGTGATAACAAAAAATTGAATAATTGAGCCGGAAAGAGTG
AAGAATAGTTTAGTCCTATAAAATAATTTTTCAAATTTAGTTTAGAAAAATCCACTAAAT
GCCACTTTTATTACTACAGATAAGAAAGAAATGTGTTTTTGCCCCTAATAAAAATTAATT
AATTCATTTTCATTCAACTGCCGAATATAATATGAATTAGGTACTTTTATTATACATAAA
ATACAATGAATAAATTAGTCTTCATATCAATTAATAAAAGAAAAATACTTACACTATCAG
GTAGTTCAGTCATGTTTGATATGCACACAATTCTATTTAACGAGATATTTTTATTGCTCA
ATAAAAATAAATTTAAATGAAAATGCATAAAGGATGAACATCGTACAAATTTTTTCACAA
CTTTTTTAGAAAATGACTACGAAAACTTCATTAGAAAGAAACAACAAAAACTAACCTAAT
CTTTATATTTCACATATCTCTTCTTCATATCCTTTTACTAACTTTAAAATTGTATGAGAT
GCTAAAATAATAAATAAGGAATTTAGTGAAGCATGAAGACATTCCAAAA

>g2198.t2 Gene=g2198 Length=148
MDDYSKYYYQRIGSDKGDFGDISSRVQLRKDLKCKSFQWYLDTIFPELFIPGDAVAQGEY
WMLSKTGEIRRDEACLDYAGSDVILYPCHGGKGNQFWNYRFDTKQLHHKSSDRCMEISSD
HQKLLMVECNSHRDAQKWYFENYDPSKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g2198.t2 CDD cd00161 RICIN 75 142 0.00
9 g2198.t2 Gene3D G3DSA:1.10.8.460 - 1 51 0.00
8 g2198.t2 Gene3D G3DSA:2.80.10.50 - 53 146 0.00
3 g2198.t2 PANTHER PTHR11675 N-ACETYLGALACTOSAMINYLTRANSFERASE 1 59 0.00
5 g2198.t2 PANTHER PTHR11675:SF112 POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 9-RELATED 1 59 0.00
2 g2198.t2 PANTHER PTHR11675 N-ACETYLGALACTOSAMINYLTRANSFERASE 59 147 0.00
4 g2198.t2 PANTHER PTHR11675:SF112 POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 9-RELATED 59 147 0.00
1 g2198.t2 Pfam PF00652 Ricin-type beta-trefoil lectin domain 58 138 0.00
10 g2198.t2 ProSiteProfiles PS50231 Lectin domain of ricin B chain profile. 59 141 17.43
7 g2198.t2 SMART SM00458 ricin_3 24 141 0.00
6 g2198.t2 SUPERFAMILY SSF50370 Ricin B-like lectins 57 142 0.00

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.

Raw TPM values