Gene loci information

Transcript annotation

  • This transcript has been annotated as Polypeptide N-acetylgalactosaminyltransferase 1.

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 g1140 g1140.t1 TTS g1140.t1 8382645 8382645
chr_3 g1140 g1140.t1 isoform g1140.t1 8383259 8385510
chr_3 g1140 g1140.t1 exon g1140.t1.exon1 8383259 8383362
chr_3 g1140 g1140.t1 cds g1140.t1.CDS1 8383259 8383362
chr_3 g1140 g1140.t1 exon g1140.t1.exon2 8383421 8383536
chr_3 g1140 g1140.t1 cds g1140.t1.CDS2 8383421 8383536
chr_3 g1140 g1140.t1 exon g1140.t1.exon3 8383613 8383698
chr_3 g1140 g1140.t1 cds g1140.t1.CDS3 8383613 8383698
chr_3 g1140 g1140.t1 exon g1140.t1.exon4 8383774 8384034
chr_3 g1140 g1140.t1 cds g1140.t1.CDS4 8383774 8384034
chr_3 g1140 g1140.t1 exon g1140.t1.exon5 8384114 8384303
chr_3 g1140 g1140.t1 cds g1140.t1.CDS5 8384114 8384303
chr_3 g1140 g1140.t1 exon g1140.t1.exon6 8384369 8384435
chr_3 g1140 g1140.t1 cds g1140.t1.CDS6 8384369 8384435
chr_3 g1140 g1140.t1 exon g1140.t1.exon7 8384510 8384636
chr_3 g1140 g1140.t1 cds g1140.t1.CDS7 8384510 8384636
chr_3 g1140 g1140.t1 exon g1140.t1.exon8 8384783 8384993
chr_3 g1140 g1140.t1 cds g1140.t1.CDS8 8384783 8384993
chr_3 g1140 g1140.t1 exon g1140.t1.exon9 8385068 8385510
chr_3 g1140 g1140.t1 cds g1140.t1.CDS9 8385068 8385510
chr_3 g1140 g1140.t1 TSS g1140.t1 8386374 8386374

Sequences

>g1140.t1 Gene=g1140 Length=1605
ATGGCATTTGAACACGAAATCGAAATGGATTTGTCAAAACAAATTCCAGGTCTATGTGAC
TTTGGGGTCGAGTGTTTTCTGAGTGGTGAAGAAATGGAGATTGGCGAAGCAAGTTATGCG
GAAAATGGAATAAATGTCATTCTAAGTGACAAAATAAGCTACAATCGTTCGCCACCCTAT
GTACAGCACGAATTATGCAAGAATGTTCACTATGACATTTTATCACTGCCTACAGCAAGT
GTCATTATAACATTCTATGAAGAGCCCTATTCTGTGCTATTACGGACAGTACATAGCGTT
TTAAATACTGCACCATCTGCGATTCTAAAAGAAATTATTCTAGTCGATGATTTCTCATCA
CGTCGTGATCTCAAAGGAAAATTGGGGTATTATGTGAAAACTCGTCTGTCATCAAAAGTG
AAATTATTCCGCATGAGAAGACAATCAGGATTAGTGCGAGCAAGGTTAGCGGGTGCTCAA
AGAGCAACGGGTTCTGTTTTGGTGTTTTTAGACGCACATTGTGAGTGCACGAGTGGATGG
TTACAGCCACTATTATCTAGAATTCATCAATCGAGAAGCTCCGTGGTTGTGCCATTAATA
GATGTTATTAATCAAAAAACTTTTGAATACGAGTCAGATGGTTATGGTTTCGATATTGGT
GGTTTCACATTAGATGGGCATTTTGATTGGCATGATGTGCCTGAAAGAGAAAGAGAACGT
CAAAGACGCGAGTGTAAAGATGAAATTGAAATTTGTCCAACATATTCACCAACAATGGCT
GGTGGTCTGTTTGCAATCTCAAGGGACTATTTTTGGGAAATTGGTTCATATGATGAGCAG
ATGGATGGATGGGGTGGCGAAAATCTGGAAATGAGTTTTCGAATCTGGATGTGCGGTGGA
ACATTAGAAACAATTCCTTGCAGTCGAATTGGACACATTTTTAGAGAGTTTCATCCATAT
AGCTTTCCAAATGACAAAGATACTCACGGAATCAATACAGTTCGAATGGCAAAAGTTTGG
ATGGACGATTATCAAGAGCTTCTTTATATGAATAGACCTGATTTGAGAAATCATCCTGAT
GTAGGCGACGTGACACACAGAAAAGTATTGAGAGATAAACTTAAGTGCAAATCCTTTGAA
TGGTATATGCAAAATATATACCCTGAAAAATTCATTCCAACAAGAAATGTTCAAAATTAT
GGACGAATATCAGCTATAGAAGACGATCGATTTTGCTTTGATGATTTACAACAGAATATT
GATGAGCCATATAATTTAGGAGTTTATTCATGCTATAAGCATGATATTGCACCATCACAA
CTTTTCTCTTATACTTATAATAAAGTATTACGAACAGAAAGAAGTTGTGCAACTATCGAT
GATCGACGAAGCACTAAATATATTGTGATGATTCCTTGCAATAGTGACGATGAAGTTACA
GATACTTGGGTTCATACTAGTTTTAATCAATTTAAACATGAACAAACGGGTCTTTGCATA
GATCGAAAAAATTTGGATAAAAATTTACTTCATGCAGCTGTATGTGATTCATTATCAAAA
ACACAAAAATGGGAATTTCAAAAGACAAAAAAGCAGAGCATTTAG

>g1140.t1 Gene=g1140 Length=534
MAFEHEIEMDLSKQIPGLCDFGVECFLSGEEMEIGEASYAENGINVILSDKISYNRSPPY
VQHELCKNVHYDILSLPTASVIITFYEEPYSVLLRTVHSVLNTAPSAILKEIILVDDFSS
RRDLKGKLGYYVKTRLSSKVKLFRMRRQSGLVRARLAGAQRATGSVLVFLDAHCECTSGW
LQPLLSRIHQSRSSVVVPLIDVINQKTFEYESDGYGFDIGGFTLDGHFDWHDVPERERER
QRRECKDEIEICPTYSPTMAGGLFAISRDYFWEIGSYDEQMDGWGGENLEMSFRIWMCGG
TLETIPCSRIGHIFREFHPYSFPNDKDTHGINTVRMAKVWMDDYQELLYMNRPDLRNHPD
VGDVTHRKVLRDKLKCKSFEWYMQNIYPEKFIPTRNVQNYGRISAIEDDRFCFDDLQQNI
DEPYNLGVYSCYKHDIAPSQLFSYTYNKVLRTERSCATIDDRRSTKYIVMIPCNSDDEVT
DTWVHTSFNQFKHEQTGLCIDRKNLDKNLLHAAVCDSLSKTQKWEFQKTKKQSI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g1140.t1 CDD cd02510 pp-GalNAc-T 80 387 0.000000
11 g1140.t1 CDD cd00161 RICIN 401 526 0.000000
9 g1140.t1 Gene3D G3DSA:3.90.550.10 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 3 394 0.000000
8 g1140.t1 Gene3D G3DSA:2.80.10.50 - 399 532 0.000000
3 g1140.t1 PANTHER PTHR11675 N-ACETYLGALACTOSAMINYLTRANSFERASE 29 532 0.000000
4 g1140.t1 PANTHER PTHR11675:SF43 POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 1 29 532 0.000000
2 g1140.t1 Pfam PF00535 Glycosyl transferase family 2 80 274 0.000000
1 g1140.t1 Pfam PF00652 Ricin-type beta-trefoil lectin domain 400 524 0.000000
10 g1140.t1 ProSiteProfiles PS50231 Lectin domain of ricin B chain profile. 399 527 14.472000
7 g1140.t1 SMART SM00458 ricin_3 398 527 0.000015
6 g1140.t1 SUPERFAMILY SSF53448 Nucleotide-diphospho-sugar transferases 57 389 0.000000
5 g1140.t1 SUPERFAMILY SSF50370 Ricin B-like lectins 384 527 0.000000

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