Gene loci information

Transcript annotation

  • This transcript has been annotated as Beta-1,4-N-acetylgalactosaminyltransferase bre-4.

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 g3533 g3533.t1 isoform g3533.t1 26231629 26233540
chr_3 g3533 g3533.t1 exon g3533.t1.exon1 26231629 26231765
chr_3 g3533 g3533.t1 cds g3533.t1.CDS1 26231629 26231765
chr_3 g3533 g3533.t1 exon g3533.t1.exon2 26231917 26232873
chr_3 g3533 g3533.t1 cds g3533.t1.CDS2 26231917 26232873
chr_3 g3533 g3533.t1 exon g3533.t1.exon3 26232940 26233032
chr_3 g3533 g3533.t1 cds g3533.t1.CDS3 26232940 26233032
chr_3 g3533 g3533.t1 exon g3533.t1.exon4 26233092 26233121
chr_3 g3533 g3533.t1 cds g3533.t1.CDS4 26233092 26233121
chr_3 g3533 g3533.t1 exon g3533.t1.exon5 26233178 26233273
chr_3 g3533 g3533.t1 cds g3533.t1.CDS5 26233178 26233273
chr_3 g3533 g3533.t1 exon g3533.t1.exon6 26233339 26233468
chr_3 g3533 g3533.t1 cds g3533.t1.CDS6 26233339 26233468
chr_3 g3533 g3533.t1 exon g3533.t1.exon7 26233535 26233540
chr_3 g3533 g3533.t1 cds g3533.t1.CDS7 26233535 26233540
chr_3 g3533 g3533.t1 TSS g3533.t1 NA NA
chr_3 g3533 g3533.t1 TTS g3533.t1 NA NA

Sequences

>g3533.t1 Gene=g3533 Length=1449
ATGGCAATACATTTGAGCCGAACGCTGGCAATAAAAGCCGCGTTGTTGGCAGGTTTGCTG
CTAATCTTTTTCAATTTAATTGGATTACGATTGGAAATCAAATTTGATCGATCGCCCGTC
AATTTATCTCATACGAGCATACCTCTCCAATGGCCAAAAAGAACGCACACAAATCACCAT
CAACAAATTAATGCACATTTAGTAGTTTCCACAAAGGAAACTCCAAAAACCGAGTTAATT
TATGGTAACTTTAGTCACAATTCAACCAGTAATCTCCAAAATAATTCAAATCTTACAAAT
GTTTATCATACAACGTTGACATCAACTGCAATTAACGATAGAGTAAAAAATTTTAGTGAA
AATGGTGATATTAAAATTAATATTAATAACCATAGTCAAATAGTAAAGAACGTAGAAAAA
TTAGATAGTCATAGTGATAAGTTAAATGGAATCGTACTGAATAATTCTTTTAGTAATGAT
ACACATGTGTCATTTCCTACATCAGTATTGCCAATTTCAACGACTGTAATTACTCACAAA
GAGATAAAGAAGCAGAAGTTGTCAAAATATCAGGATTTTGATGCAAGTCTTGTTCAAGAT
GGAAGCATTTTCAATAGTATCATGAAAGTATTTGGTATTAATCAATGTCCAGCAACGCCT
ACCGATCTTATCGGTCCAATTGAAGTTGATACTAGTCCAGAATATTTAGAGAATGTTGAG
AAACGTCTCTCCAATAAAATTCAACCAGGTGGACGTTATAAGCCAGAGGACTGTAGAGCA
CGTGATCGTGTCGCTATTGTTATTCCATTTCGTGACAGGAAGCAACACTTGCCAATTTTT
TTAAAAAATCTTCACCCGTTTTTAATGAAGCAACAAATTAATTATGGAATATTTTTGATC
GAGCAATCGTCTGATGGAAACTTTAATCGCGCAAAACTCTTCAATGTTGGATTTGTTGAA
GCACTAAAATTATATGATTGGGATTGTTTCATTTTTCATGATGTTGATCTTTTACCACTG
GATGATAGAAACTTGTATACGTGCCCTGATCAGCCACGACATATGAGTGTTGCCGTTGAT
ACTTTTGATTTCAAATTACCGTATGCCACCATATTTGGGGGAGTCTCATCAATGACCACG
AAACAATTTAAAGCTGTCAATGGATTTTCAAACTCTTTTTGGGGATGGGGTGGCGAGGAT
GATGACTTGTCACGAAGATTGAGACATTTTGGCTATCATATTGCGCGTTATCCTATCAAC
ATTGCTCGCTACACTATGTTAACTCATAAGAAAGAAAAAGCGAATCCAAAAAGATATGAG
AAACTTGTGACTGGCGCAAATAGATTCAGCACAGATGGTTTGAACTCATTAAAATACAAA
GTTCTTGATTTTCAGTTGAAGCCCCTTTACACATATTTTCTTGTTGAAATAACGCCTGAA
ACAAGTTGA

>g3533.t1 Gene=g3533 Length=482
MAIHLSRTLAIKAALLAGLLLIFFNLIGLRLEIKFDRSPVNLSHTSIPLQWPKRTHTNHH
QQINAHLVVSTKETPKTELIYGNFSHNSTSNLQNNSNLTNVYHTTLTSTAINDRVKNFSE
NGDIKININNHSQIVKNVEKLDSHSDKLNGIVLNNSFSNDTHVSFPTSVLPISTTVITHK
EIKKQKLSKYQDFDASLVQDGSIFNSIMKVFGINQCPATPTDLIGPIEVDTSPEYLENVE
KRLSNKIQPGGRYKPEDCRARDRVAIVIPFRDRKQHLPIFLKNLHPFLMKQQINYGIFLI
EQSSDGNFNRAKLFNVGFVEALKLYDWDCFIFHDVDLLPLDDRNLYTCPDQPRHMSVAVD
TFDFKLPYATIFGGVSSMTTKQFKAVNGFSNSFWGWGGEDDDLSRRLRHFGYHIARYPIN
IARYTMLTHKKEKANPKRYEKLVTGANRFSTDGLNSLKYKVLDFQLKPLYTYFLVEITPE
TS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g3533.t1 CDD cd00899 b4GalT 261 476 1.96869E-119
10 g3533.t1 Gene3D G3DSA:3.90.550.10 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 206 480 2.7E-114
3 g3533.t1 PANTHER PTHR19300 BETA-1,4-GALACTOSYLTRANSFERASE 174 480 4.9E-127
4 g3533.t1 PANTHER PTHR19300:SF52 BETA4GALNACTA 174 480 4.9E-127
7 g3533.t1 PRINTS PR02050 Beta-1,4-galactosyltransferase family signature 298 317 7.6E-37
6 g3533.t1 PRINTS PR02050 Beta-1,4-galactosyltransferase family signature 329 348 7.6E-37
5 g3533.t1 PRINTS PR02050 Beta-1,4-galactosyltransferase family signature 366 387 7.6E-37
8 g3533.t1 PRINTS PR02050 Beta-1,4-galactosyltransferase family signature 388 406 7.6E-37
2 g3533.t1 Pfam PF13733 N-terminal region of glycosyl transferase group 7 216 349 5.4E-56
1 g3533.t1 Pfam PF02709 N-terminal domain of galactosyltransferase 353 430 2.9E-29
12 g3533.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 28 -
13 g3533.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 12 -
14 g3533.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 13 24 -
15 g3533.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 25 28 -
11 g3533.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 29 482 -
9 g3533.t1 SUPERFAMILY SSF53448 Nucleotide-diphospho-sugar transferases 215 478 1.31E-57
17 g3533.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

GOID TERM ONTOLOGY
GO:0016757 glycosyltransferase activity MF
GO:0005975 carbohydrate metabolic process BP

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