Gene loci information

Transcript annotation

  • This transcript has been annotated as Polypeptide N-acetylgalactosaminyltransferase 3.

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_1 g13318 g13318.t1 isoform g13318.t1 29165467 29169903
chr_1 g13318 g13318.t1 exon g13318.t1.exon1 29165467 29165679
chr_1 g13318 g13318.t1 cds g13318.t1.CDS1 29165467 29165679
chr_1 g13318 g13318.t1 exon g13318.t1.exon2 29167263 29167416
chr_1 g13318 g13318.t1 cds g13318.t1.CDS2 29167263 29167416
chr_1 g13318 g13318.t1 exon g13318.t1.exon3 29167473 29167602
chr_1 g13318 g13318.t1 cds g13318.t1.CDS3 29167473 29167602
chr_1 g13318 g13318.t1 exon g13318.t1.exon4 29167660 29169109
chr_1 g13318 g13318.t1 cds g13318.t1.CDS4 29167660 29169109
chr_1 g13318 g13318.t1 exon g13318.t1.exon5 29169754 29169903
chr_1 g13318 g13318.t1 cds g13318.t1.CDS5 29169754 29169903
chr_1 g13318 g13318.t1 TTS g13318.t1 29170253 29170253
chr_1 g13318 g13318.t1 TSS g13318.t1 NA NA

Sequences

>g13318.t1 Gene=g13318 Length=2097
ATGAAAGTTTGCAGACATCATGATGAAATTGATTGTTTTGGTGCTATTCTGCATAATTGG
CCAGCATACAATGAAAATGATACACATGTTGATGAACTTTGTGGATGTTTAAAGAATTGC
AATGATATTTTTTATTCAATGAAAATTCAAATAGAGAAGAAAACACCAGAAAATTACACT
GGAATTGCAATGAGTTTTATTTTTGAAGATAGAATAATAGAATTACAAGATAGCAGATAT
GCACATCGTGCACGCGGAAGAATTCCACAAATTGTAGGTCATTACATGCCTGGTGCAAGT
GTTAATTTCAGCAATGATTTTTTAAACTCAAACAATTATGATCCAATTGCTGGTGAAGGA
GAAAATGGCAATCCGGTTATCATTCCATCAAAAGATCTTCTTAAAATGCAACAACTCTTC
CAAATAAATCGTTTTAATTTACTTGCAAGTGATAGAATCTCTATAAATAGAACACTTCAG
GATGTTAGAAATAATGTATGCAAAACCAAAACTTATCCAACGAATCTTCCAACCACATCG
ATCATAATTGTATTTCATAACGAAGCGTGGTCTGTTTTATTGCGCACACTATGGTCTGTG
ATTAATCGATCTCGTGCAGATCTAGTCCATGAGATTTTGCTCATTGATGATGCGAGTACA
CGAACATTCCTGAAAGAGCAGCTAGATGAATATGTGGCGAAATTGCCAATTCCAACTCGA
GTATTGCGATTACAAAATCGCGAGGGATTAGTGAGTGCAAGACTGTTGGGTGCAAAGAAT
GCAAAAGGCGAAGTATTGACCTTCCTTGATGCTCACTGTGAGTGCAATACTGGTTGGTTA
GAGCCGCTATTGAAGCGAGTTAAAGACAATCGAAAAGTTGTCATTTGTCCAGTCATCGAC
ATCATTTCTGATGATAATTTTAGTTATATTAAAAGTTTTGACTTTCATTGGGGCGCATTC
AATTGGGAACTTCATTTTCGATGGTTTATGCTTGGCGATGAAGAGCTCAAGAAAAGACAA
AAAGATGTTAGTGCACCATTTAAAACTCCTGCATTTGCTGGTGGATTATTTTCAATAAAT
CGTCAATATTTTTTTGAAATTGGCAGTTATGATGAAAGTATGAGAATTTGGGGTGGCGAT
AATATTGAAATGAGCATGAGAATATGGATGTGTGGCGGCAGTATTGAAATTGCACCGTGT
TCACATGTTGGTCATCTTTTTCGAAAAAGTTCACCTTATACTTTCCCTGGTGGTGTCAAC
GAAATTTTAAATAGAAATTTAGCACGTGTTGCTGATGTTTGGATGGATCAATGGAAAGAA
TTTTATTATAAATTTAATCATAATGCAAATTCTTTAAGAGCAACATTGAATACAACTGAA
AGAGTAATTTTAAGGCAAAAACTTCAATGTAAACCTTTTACTTGGTATTTACAGAATGTT
TGGAAAGAAAATTTCTTTCCTGCTAAAAATCGCTTCTTTGGAAGAATTCAAATTGCAAAT
TTGACTACAATTGGACCTGAATATAGAAAATATTATGACATCATTCAGGAGTTTAGTCGT
GTGATTCATTTTCAAGAACAAAGTATCGATGAGCGCTGGAACAAATTGATTAAATATTTC
AACAAGCGAACTGAGGCAATCAATGAGCTCTTTCGTCATAATTCCAATGATTATTTGTGT
TTGCAAAAACCCAAGACTAACAACGCTGTGACTCCATATGGCCAAACTTTTATACGAAAA
TGCTCAAAACTTTATGATAGTTTAGATGAAATGTTTGTCATTACAATTGATGGAAAAATT
ATGACAAATGAAAATTTGTGCTTGGATTCATTTAAAATTCATACATCGGATGACTCGAAT
GATGAAAAGAATGGAAAGGATGAGAATTATGCAAAAATGGTTACGTGCTCAACTAAAAGT
ACGCAGTACTTTATTTATAATACTAATACACTCCAATTATTACAAGCGAATACAGGCATG
TGTTTGCAAGGAACCAACATTCCAGCTGAAAATGAAAGTTACAAAATATTGCTGACCGAT
TGCAGTGAAAACAATAAACAACAGAAGTGGATTCTTTTTCCAGTCGAATGGCATTGA

>g13318.t1 Gene=g13318 Length=698
MKVCRHHDEIDCFGAILHNWPAYNENDTHVDELCGCLKNCNDIFYSMKIQIEKKTPENYT
GIAMSFIFEDRIIELQDSRYAHRARGRIPQIVGHYMPGASVNFSNDFLNSNNYDPIAGEG
ENGNPVIIPSKDLLKMQQLFQINRFNLLASDRISINRTLQDVRNNVCKTKTYPTNLPTTS
IIIVFHNEAWSVLLRTLWSVINRSRADLVHEILLIDDASTRTFLKEQLDEYVAKLPIPTR
VLRLQNREGLVSARLLGAKNAKGEVLTFLDAHCECNTGWLEPLLKRVKDNRKVVICPVID
IISDDNFSYIKSFDFHWGAFNWELHFRWFMLGDEELKKRQKDVSAPFKTPAFAGGLFSIN
RQYFFEIGSYDESMRIWGGDNIEMSMRIWMCGGSIEIAPCSHVGHLFRKSSPYTFPGGVN
EILNRNLARVADVWMDQWKEFYYKFNHNANSLRATLNTTERVILRQKLQCKPFTWYLQNV
WKENFFPAKNRFFGRIQIANLTTIGPEYRKYYDIIQEFSRVIHFQEQSIDERWNKLIKYF
NKRTEAINELFRHNSNDYLCLQKPKTNNAVTPYGQTFIRKCSKLYDSLDEMFVITIDGKI
MTNENLCLDSFKIHTSDDSNDEKNGKDENYAKMVTCSTKSTQYFIYNTNTLQLLQANTGM
CLQGTNIPAENESYKILLTDCSENNKQQKWILFPVEWH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g13318.t1 CDD cd02510 pp-GalNAc-T 180 481 0.0000000
9 g13318.t1 Gene3D G3DSA:3.90.550.10 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 103 488 0.0000000
8 g13318.t1 Gene3D G3DSA:2.80.10.50 - 547 696 0.0000000
3 g13318.t1 PANTHER PTHR11675 N-ACETYLGALACTOSAMINYLTRANSFERASE 82 697 0.0000000
4 g13318.t1 PANTHER PTHR11675:SF118 POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 3 82 697 0.0000000
2 g13318.t1 Pfam PF00535 Glycosyl transferase family 2 180 364 0.0000000
1 g13318.t1 Pfam PF00652 Ricin-type beta-trefoil lectin domain 554 690 0.0000000
10 g13318.t1 ProSiteProfiles PS50231 Lectin domain of ricin B chain profile. 547 693 15.7730000
7 g13318.t1 SMART SM00458 ricin_3 548 693 0.0000006
6 g13318.t1 SUPERFAMILY SSF53448 Nucleotide-diphospho-sugar transferases 156 483 0.0000000
5 g13318.t1 SUPERFAMILY SSF50370 Ricin B-like lectins 552 692 0.0000000

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