Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Lactase-phlorizin hydrolase.

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 g1437 g1437.t1 isoform g1437.t1 10981530 10983981
chr_3 g1437 g1437.t1 exon g1437.t1.exon1 10981530 10981966
chr_3 g1437 g1437.t1 cds g1437.t1.CDS1 10981530 10981966
chr_3 g1437 g1437.t1 exon g1437.t1.exon2 10982091 10982187
chr_3 g1437 g1437.t1 cds g1437.t1.CDS2 10982091 10982187
chr_3 g1437 g1437.t1 exon g1437.t1.exon3 10982577 10982637
chr_3 g1437 g1437.t1 cds g1437.t1.CDS3 10982577 10982637
chr_3 g1437 g1437.t1 exon g1437.t1.exon4 10982699 10982835
chr_3 g1437 g1437.t1 cds g1437.t1.CDS4 10982699 10982835
chr_3 g1437 g1437.t1 exon g1437.t1.exon5 10982934 10983052
chr_3 g1437 g1437.t1 cds g1437.t1.CDS5 10982934 10983052
chr_3 g1437 g1437.t1 exon g1437.t1.exon6 10983116 10983141
chr_3 g1437 g1437.t1 cds g1437.t1.CDS6 10983116 10983141
chr_3 g1437 g1437.t1 exon g1437.t1.exon7 10983740 10983981
chr_3 g1437 g1437.t1 cds g1437.t1.CDS7 10983740 10983981
chr_3 g1437 g1437.t1 TSS g1437.t1 NA NA
chr_3 g1437 g1437.t1 TTS g1437.t1 NA NA

Sequences

>g1437.t1 Gene=g1437 Length=1119
ATGACGATTGATGATTATGATAGAATTGAATATTTGAATCTTCATTTAAAAGCTTTATCT
CAAGCAATTGATGCTAGCTGTAATGTAAAAGCTTACACAGTTTGGAGTTTAATTGATAAT
TTTGAATGGATGAGAGGATATACTGAAAGATTTGGAATTTATGCAATTAATTTTACTGAT
CCTGAAAGACAAAGAATTCCAAAGAAATCAGTTGCACTTTTTAAAGATTTAATGCAAAAT
ATTAATTTTGTTTGGGGTGCTGCTTCAGCAAGTTATCAAATCGAAGGAGCATGGAATGTA
GATGGAAGAATTCCTAGTATTTGGGACACAGCATCACATAAAAATAATTCAAGTGTTGTT
GATGGATCAACTGTTATGATGCCACATTTTAAAACGTATCGATTTTCAATTGCTTGGCCA
AGAGTATTGACAAAAACAAACCAAGTTAATCAAGCTGGAATTGATTATTATAGTAAATTA
ATTGATCGATTGAAAGAAGAAGAAATTAAACCAATGGTCACAATGTATCATTGGGACTTA
CCTCAATATCTTCAAGATTTAGGAGGTTGGACAAATCCAGCTATTCTTGGTCGTTATGCA
AATCCAATTTATTCAGTTGATGATTATCCAAGAGTTATGCGTGAAGCAATTGATCAAAGA
GTGAAAATGAAGGGAGAAGATGCTGATAGTGATAGTGAAATTCATTCATTTCATGATGAC
AGTTGGAAAAGAAGTGCGAGTTCGTGGTTAGTGTCGGTTCCTGAAGGTTTATATCATCTA
TTACTTTGGATAAAAGATCATTACAATAATCCTTTAGTTTATATTACTGAAAATGGTTGG
TCAGATTTACCAATGACGACTGAAGATGATGGTCGTGTTGAATATTTAAGAGAACATCTT
GCTACAATGTCTCGAGCAATTACTGATGGTTGTAGAGTTGAAGCTTATACAGTTTGGAGT
TTAACAGATAATTTCGAATGGATGAGAGGTTACACTGAAAGATTTGGAATTTATGCAATT
AATTTTACTGATCCTGAAAGAAAAAGAATTCCAAAGAATTCAGTTGATTTAATGAAACAA
GTTGTTCGTGACAATTTTGTTGAAGTTGAAAAAGATTAA

>g1437.t1 Gene=g1437 Length=372
MTIDDYDRIEYLNLHLKALSQAIDASCNVKAYTVWSLIDNFEWMRGYTERFGIYAINFTD
PERQRIPKKSVALFKDLMQNINFVWGAASASYQIEGAWNVDGRIPSIWDTASHKNNSSVV
DGSTVMMPHFKTYRFSIAWPRVLTKTNQVNQAGIDYYSKLIDRLKEEEIKPMVTMYHWDL
PQYLQDLGGWTNPAILGRYANPIYSVDDYPRVMREAIDQRVKMKGEDADSDSEIHSFHDD
SWKRSASSWLVSVPEGLYHLLLWIKDHYNNPLVYITENGWSDLPMTTEDDGRVEYLREHL
ATMSRAITDGCRVEAYTVWSLTDNFEWMRGYTERFGIYAINFTDPERKRIPKNSVDLMKQ
VVRDNFVEVEKD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g1437.t1 Gene3D G3DSA:3.20.20.80 Glycosidases 2 81 1.6E-28
20 g1437.t1 Gene3D G3DSA:3.20.20.80 Glycosidases 82 201 2.8E-42
18 g1437.t1 Gene3D G3DSA:3.20.20.80 Glycosidases 203 372 8.7E-50
4 g1437.t1 PANTHER PTHR10353:SF36 CYTOSOLIC BETA-GLUCOSIDASE 3 80 4.1E-109
7 g1437.t1 PANTHER PTHR10353 GLYCOSYL HYDROLASE 3 80 4.1E-109
6 g1437.t1 PANTHER PTHR10353:SF36 CYTOSOLIC BETA-GLUCOSIDASE 82 201 4.1E-109
9 g1437.t1 PANTHER PTHR10353 GLYCOSYL HYDROLASE 82 201 4.1E-109
5 g1437.t1 PANTHER PTHR10353:SF36 CYTOSOLIC BETA-GLUCOSIDASE 226 366 4.1E-109
8 g1437.t1 PANTHER PTHR10353 GLYCOSYL HYDROLASE 226 366 4.1E-109
10 g1437.t1 PRINTS PR00131 Glycosyl hydrolase family 1 signature 148 162 2.5E-15
11 g1437.t1 PRINTS PR00131 Glycosyl hydrolase family 1 signature 273 281 2.5E-15
13 g1437.t1 PRINTS PR00131 Glycosyl hydrolase family 1 signature 289 300 2.5E-15
12 g1437.t1 PRINTS PR00131 Glycosyl hydrolase family 1 signature 310 327 2.5E-15
14 g1437.t1 PRINTS PR00131 Glycosyl hydrolase family 1 signature 334 346 2.5E-15
3 g1437.t1 Pfam PF00232 Glycosyl hydrolase family 1 2 80 3.1E-24
2 g1437.t1 Pfam PF00232 Glycosyl hydrolase family 1 82 200 3.8E-40
1 g1437.t1 Pfam PF00232 Glycosyl hydrolase family 1 208 365 5.2E-38
17 g1437.t1 ProSitePatterns PS00653 Glycosyl hydrolases family 1 N-terminal signature. 83 97 -
15 g1437.t1 SUPERFAMILY SSF51445 (Trans)glycosidases 3 80 2.11E-26
16 g1437.t1 SUPERFAMILY SSF51445 (Trans)glycosidases 82 367 1.69E-84

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:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds MF
GO:0005975 carbohydrate metabolic process BP

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. There were no conditions that were differentially expressed