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.t1 isoform g2198.t1 15915963 15939486
chr_3 g2198 g2198.t1 exon g2198.t1.exon1 15915963 15916440
chr_3 g2198 g2198.t1 cds g2198.t1.CDS1 15915963 15916440
chr_3 g2198 g2198.t1 exon g2198.t1.exon2 15916507 15917126
chr_3 g2198 g2198.t1 cds g2198.t1.CDS2 15916507 15917126
chr_3 g2198 g2198.t1 exon g2198.t1.exon3 15937140 15937235
chr_3 g2198 g2198.t1 cds g2198.t1.CDS3 15937140 15937235
chr_3 g2198 g2198.t1 exon g2198.t1.exon4 15937291 15937366
chr_3 g2198 g2198.t1 cds g2198.t1.CDS4 15937291 15937366
chr_3 g2198 g2198.t1 exon g2198.t1.exon5 15937427 15937585
chr_3 g2198 g2198.t1 cds g2198.t1.CDS5 15937427 15937585
chr_3 g2198 g2198.t1 exon g2198.t1.exon6 15937728 15937879
chr_3 g2198 g2198.t1 cds g2198.t1.CDS6 15937728 15937879
chr_3 g2198 g2198.t1 exon g2198.t1.exon7 15937940 15937972
chr_3 g2198 g2198.t1 cds g2198.t1.CDS7 15937940 15937972
chr_3 g2198 g2198.t1 exon g2198.t1.exon8 15938089 15938199
chr_3 g2198 g2198.t1 cds g2198.t1.CDS8 15938089 15938199
chr_3 g2198 g2198.t1 exon g2198.t1.exon9 15938505 15938609
chr_3 g2198 g2198.t1 cds g2198.t1.CDS9 15938505 15938609
chr_3 g2198 g2198.t1 exon g2198.t1.exon10 15939157 15939264
chr_3 g2198 g2198.t1 cds g2198.t1.CDS10 15939157 15939264
chr_3 g2198 g2198.t1 exon g2198.t1.exon11 15939325 15939486
chr_3 g2198 g2198.t1 cds g2198.t1.CDS11 15939325 15939486
chr_3 g2198 g2198.t1 TSS g2198.t1 NA NA
chr_3 g2198 g2198.t1 TTS g2198.t1 NA NA

Sequences

>g2198.t1 Gene=g2198 Length=2100
ATGATTTGGAGACGAAAATCATCGCTGTTCAAAATTCTACTCGCAATTTTAGCAATATGG
TTCACAGTCGTGTTCTTTTTCTCTGATAATAATCGTTCCGATACCAATGTTGTGTTATCG
CCACAATTGTTGACACAACATGATGAAAACAATGCCAAAGCGTACGATAAAAATAATAAG
TTAAAGAATTTCATCATTGATAGCTATAAAGATGCACATGAAGGTTTTGCTAATGCGATA
GCGAACAAAAAATTTCCACAACTGAATCCATTTGAAAGTCAAAAGCAAGAGGTCGATGAG
AATGAAATGATTAACGAAATTGCGGGTGAGCATGAAGAGGAAGTAAGGCAGGAAGAAGAA
GAAAGACGTCCGTCAACAAAAGCTAAAGTTCCATCGAAAAAGAGATTTGGCAATAAAGAT
GGTGATGAAAATGTAGGCTTTATTCCTCCACCCAACGATCTCGGATTAGAGAGTCCAGGT
GAACTTGGAAAGCCAGTAACACTTCCAAATAATTTAACCGGTGAAGTTAAGAAATTGGTC
GATGAAGGATGGCTTAAGAATGCTTTTAATCAATACGTCTCTGATCTCATTAGTATTCGT
AGAAGCCTTCCCGATCCTAGAACAAAATGGTGCAAAGATGCTGAAAAGGATTATGTTCAA
GACCTTCCTCAAACATCTGTGATTGTTACATTCCATAATGAAGCATGGTCGACGCTATTG
CGATCTGTTCACTCCATTTTAGATCGTTCGCCAGAAAATTTAATTAAGGAAATTATTTTA
GTTGACGATTTCTCAGACATGCCACATTTAAGAAAGCAATTGGAAGATTATCTTCTTAAC
TACCCTAAAGTGAAAATTATTCGTGCTAAGAAACGAGAAGGTCTCATAAGAGCACGTTTG
TTAGGAGCTGTAGCAGCGACTGCACCAGTTTTGACATTCTTAGACTCGCATATTGAATGC
ACGACTGGTTGGTTAGAACCGCTTTTAGATAGAATTGCTCGAAATTCCACAACTGTTGTT
TGTCCTGTCATTGATGTAATTGACGATACTACATTGCAATACCATTATCATGATTCAACT
GGTGTACAAGTTGGAGGGTTCGATTGGAACCTCCAATTTAACTGGCATCCAGTACCTGAA
TCTGAAAGAAAGCGTCATAAAGACCCATCTGAACCAGTATGGAGCCCAACTATGGCTGGA
GGTTTATTTTCAATTGATAAAGCTTTTTTTGAGAGACTAGGAATGTATGATGATGGTTTT
GATATTTGGGGTGGTGAAAATCTTGAATTAAGTTTCAAAACTTGGATGTGCGGCGGCACT
TTAGAAATTATACCGTGTTCGCACGTGGGACATATTTTTAGAAAACGTTCGCCTTATAAA
TGGCGAACTGGAGTGAATGTACTAAGAAGAAATTCAATTAGATTGGCTGAGGTATGGATG
GATGATTACTCGAAATATTATTATCAAAGAATTGGATCAGATAAGGGTGATTTTGGTGAT
ATCAGCTCTAGAGTTCAACTTAGAAAGGATTTAAAATGTAAAAGCTTCCAATGGTATCTC
GACACAATCTTCCCAGAATTGTTTATACCAGGTGATGCAGTGGCACAAGGAGAGGTAAGA
AACTTAGGATATGGAAATCGATCATGTCTTGATGCTCAAGGTGGTAAAAAAGGGCTTCGA
AAGCCTGTTTCTCTATATCCCTGTCATCGTCAAGGTGGAAATCAAATCCGAAATAATGCT
TCAAATATGTGCGTTGATTCTGCGGTGAAACCGGATGATTTGCAAGGGCCCGTTGGTTTA
TGGCCTTGTCATAATCAAGGTGGCAATCAGTATTGGATGCTCTCAAAAACTGGAGAGATT
CGCAGAGACGAAGCATGTTTGGATTATGCTGGCTCTGATGTTATTCTTTATCCATGCCAT
GGTGGTAAAGGCAATCAGTTCTGGAATTATCGATTTGACACAAAGCAACTTCATCACAAA
TCATCAGATAGATGTATGGAAATCAGTAGTGATCATCAGAAACTATTGATGGTTGAATGC
AATTCACATCGTGATGCACAAAAATGGTACTTTGAAAATTACGACCCAAGCAAACTGTAA

>g2198.t1 Gene=g2198 Length=699
MIWRRKSSLFKILLAILAIWFTVVFFFSDNNRSDTNVVLSPQLLTQHDENNAKAYDKNNK
LKNFIIDSYKDAHEGFANAIANKKFPQLNPFESQKQEVDENEMINEIAGEHEEEVRQEEE
ERRPSTKAKVPSKKRFGNKDGDENVGFIPPPNDLGLESPGELGKPVTLPNNLTGEVKKLV
DEGWLKNAFNQYVSDLISIRRSLPDPRTKWCKDAEKDYVQDLPQTSVIVTFHNEAWSTLL
RSVHSILDRSPENLIKEIILVDDFSDMPHLRKQLEDYLLNYPKVKIIRAKKREGLIRARL
LGAVAATAPVLTFLDSHIECTTGWLEPLLDRIARNSTTVVCPVIDVIDDTTLQYHYHDST
GVQVGGFDWNLQFNWHPVPESERKRHKDPSEPVWSPTMAGGLFSIDKAFFERLGMYDDGF
DIWGGENLELSFKTWMCGGTLEIIPCSHVGHIFRKRSPYKWRTGVNVLRRNSIRLAEVWM
DDYSKYYYQRIGSDKGDFGDISSRVQLRKDLKCKSFQWYLDTIFPELFIPGDAVAQGEVR
NLGYGNRSCLDAQGGKKGLRKPVSLYPCHRQGGNQIRNNASNMCVDSAVKPDDLQGPVGL
WPCHNQGGNQYWMLSKTGEIRRDEACLDYAGSDVILYPCHGGKGNQFWNYRFDTKQLHHK
SSDRCMEISSDHQKLLMVECNSHRDAQKWYFENYDPSKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g2198.t1 CDD cd02510 pp-GalNAc-T 226 524 1.29704E-175
17 g2198.t1 CDD cd00161 RICIN 575 691 3.40634E-23
13 g2198.t1 Coils Coil Coil 101 121 -
12 g2198.t1 Gene3D G3DSA:3.90.550.10 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 151 530 8.8E-170
11 g2198.t1 Gene3D G3DSA:2.80.10.50 - 532 575 1.6E-6
10 g2198.t1 Gene3D G3DSA:2.80.10.50 - 576 697 7.7E-39
21 g2198.t1 MobiDBLite mobidb-lite consensus disorder prediction 109 157 -
22 g2198.t1 MobiDBLite mobidb-lite consensus disorder prediction 109 141 -
4 g2198.t1 PANTHER PTHR11675 N-ACETYLGALACTOSAMINYLTRANSFERASE 2 577 2.6E-252
6 g2198.t1 PANTHER PTHR11675:SF112 POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 9-RELATED 2 577 2.6E-252
3 g2198.t1 PANTHER PTHR11675 N-ACETYLGALACTOSAMINYLTRANSFERASE 583 698 2.6E-252
5 g2198.t1 PANTHER PTHR11675:SF112 POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 9-RELATED 583 698 2.6E-252
2 g2198.t1 Pfam PF00535 Glycosyl transferase family 2 226 407 1.2E-32
1 g2198.t1 Pfam PF00652 Ricin-type beta-trefoil lectin domain 575 689 1.3E-29
14 g2198.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
16 g2198.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 28 -
15 g2198.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 29 699 -
23 g2198.t1 ProSiteProfiles PS50231 Lectin domain of ricin B chain profile. 570 692 26.483
20 g2198.t1 SMART SM00458 ricin_3 570 692 3.1E-28
9 g2198.t1 SUPERFAMILY SSF53448 Nucleotide-diphospho-sugar transferases 201 526 2.06E-54
8 g2198.t1 SUPERFAMILY SSF50370 Ricin B-like lectins 522 587 1.38E-6
7 g2198.t1 SUPERFAMILY SSF50370 Ricin B-like lectins 575 693 2.56E-33
19 g2198.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 7 29 -

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

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.

Raw TPM values