Gene loci information

Transcript annotation

  • This transcript has been annotated as Trehalase.

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_4 g17178 g17178.t18 TTS g17178.t18 12730043 12730043
chr_4 g17178 g17178.t18 isoform g17178.t18 12730044 12732927
chr_4 g17178 g17178.t18 exon g17178.t18.exon1 12730044 12730608
chr_4 g17178 g17178.t18 cds g17178.t18.CDS1 12730453 12730608
chr_4 g17178 g17178.t18 exon g17178.t18.exon2 12730787 12731185
chr_4 g17178 g17178.t18 cds g17178.t18.CDS2 12730787 12731185
chr_4 g17178 g17178.t18 exon g17178.t18.exon3 12731252 12731830
chr_4 g17178 g17178.t18 cds g17178.t18.CDS3 12731252 12731830
chr_4 g17178 g17178.t18 exon g17178.t18.exon4 12732419 12732642
chr_4 g17178 g17178.t18 cds g17178.t18.CDS4 12732419 12732642
chr_4 g17178 g17178.t18 exon g17178.t18.exon5 12732711 12732927
chr_4 g17178 g17178.t18 cds g17178.t18.CDS5 12732711 12732768
chr_4 g17178 g17178.t18 TSS g17178.t18 NA NA

Sequences

>g17178.t18 Gene=g17178 Length=1984
AGATGGCTCGACTTTATAATGATTCAAAGACTTTTGTTGATATGAAACTCAAAAATCCAC
CACATGAGACTATACAGCTTTTTAATAATTTTATGGCTGATTTTCCTGATGGTTTACCCG
ACACTGATAAACTTCGACAATGGGTTGAAGAACATTTTGATGAACCTGGTTCTGAATTTG
AGCAATGGACGCCCGATGATTTTCAAAAATCACCAAAATAAAATAAGTGATAAAAACTTC
CGTGATTTTGCAAGTGAATTAAATGGAATTTGGTTAGAATTGGGAAGAAAAATGAAGCCA
GATGTAAAAATTAATGAAGATCACTATTCAATAATTCATGTCGATAATCCAGTAATTGTG
CCAGGTGGAAGATTTAGAGAATTCTATTATTGGGATTCTTATTGGGTCATTCGAGGTTTA
CTGCTGTGTGAAATGTACAATACAACAAAAGGAATGCTTGAAAATTTCATGTCAATAGTA
ACACGTTACGGTTTTATTCCAAATGGTGGCAGAATATATTATTCGTTACGTTCTCAGCCG
CCACTTCTTGCACCAATGGTCAAAACTTATGTTGAAACCACAAATGATATTGATTTTGCT
GTAAAATATGTTGATGTACTTGCATTAGAATTTAATTATTGGTTGGCAAATCACACAGTA
CAAGTTAAAGGACACACATTAGCAAGATATGGTGATAAATCAAATGGACCAAGACCAGAA
AGTTATAGAGAAGATATAGAAACAGGAAGTGGTTTTCAAAGTGCAAAGGACAAAGAAGAA
CATTATGCAGAATTGAAAGCAGCTGCTGAAAGTGGAATGGACTTTTCATCGCGATGGTTT
ATCAATGATGAAGGCACAAATGTTGGAACACTTGAGAATTTAAAGACAAGATATATCATA
CCAGTTGAATTAAATGCTATTTTATATTGGAATGCCGTCATTATTGCTGAATTTTATGCT
ATTGCTGGCAATGAAACTAGAAAAAAAGAATACCTTAGAATAGCTAAGGACTTTATGGAT
GCTGTAAATGAAGTGTTATGGGATGAAGAAACTGGAGCATGGCTCGATTATGATCTGATA
AATGAAAAACACAGAAATTATTTCGTTCCAACAAATCTTTCGCCACTTTGGATGAAATGC
TATGATATAACAAAACGCGAACACATTGCCTCAAAAGTCTTACAGTATATTGATAATTTA
AAACTTGATGATTATCCTGGTGGTGTTCCAACAACTCTCATGAACAGTGGTGAACAATGG
GATTGGCCAAATGTATGGGCACCAACGCAACATATTTTAATTGTTGGATTAGAAAATCTT
GGTGTTAAAGAGGCTCAAGAAAAAGCACAAGATTATGCACAACGATGGGTGCATGGCAAT
TATATTGCATTCAAAGAGAGTGGAGCTATGTATGAAAAGTATCTTGCAACAGAACTCGGC
GGACATGGTGGAGGTGGTGAATATGAAGTCCAAAAAGGCTTCGGATGGACAAATGGTGTA
ATTCTTGATCTCCTTGATCGTTATGGCGAAGTTTTAAGTTCTTCAGGTGAAGAATCAAAT
TTGATAAAGGAATAAAAAACTTTGCGAATCATTTTCATCACACAAAAAAAAATTTCGTGC
ACATTTGTCCTATAATTATACACTGACACCCACCACACCACCATTTCATCATCTTTGTTA
TTTGTTAATGTGAAGTCAAAAAAAAAGAATTTCTTAGGTCGTTGAGATAAAATTTAGGAA
ATTTGTTGTATCTAAAAATAAAATCATTCATTCAATTTAAGTTTCTGAGTTAGTTTAGCT
GGTGATAATTTTTTTTGTTTAATTTCTCTCTCATTTATGACGTAAGCTTTAATGACACAA
ATTAAAATAGTATATAGATGAACTACCGCGATGAAAAAAAGTTATGAGTGATAATCAATT
AATTGTGTCTTTGCACTTCATATTAAATTTATTTCATAATGACGACAAATTTAAATAAAA
ATTC

>g17178.t18 Gene=g17178 Length=471
MNLVLNLSNGRPMIFKNHQNKISDKNFRDFASELNGIWLELGRKMKPDVKINEDHYSIIH
VDNPVIVPGGRFREFYYWDSYWVIRGLLLCEMYNTTKGMLENFMSIVTRYGFIPNGGRIY
YSLRSQPPLLAPMVKTYVETTNDIDFAVKYVDVLALEFNYWLANHTVQVKGHTLARYGDK
SNGPRPESYREDIETGSGFQSAKDKEEHYAELKAAAESGMDFSSRWFINDEGTNVGTLEN
LKTRYIIPVELNAILYWNAVIIAEFYAIAGNETRKKEYLRIAKDFMDAVNEVLWDEETGA
WLDYDLINEKHRNYFVPTNLSPLWMKCYDITKREHIASKVLQYIDNLKLDDYPGGVPTTL
MNSGEQWDWPNVWAPTQHILIVGLENLGVKEAQEKAQDYAQRWVHGNYIAFKESGAMYEK
YLATELGGHGGGGEYEVQKGFGWTNGVILDLLDRYGEVLSSSGEESNLIKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g17178.t18 Gene3D G3DSA:1.50.10.10 - 13 468 7.6E-167
2 g17178.t18 PANTHER PTHR23403 TREHALASE 20 458 1.5E-183
3 g17178.t18 PANTHER PTHR23403:SF1 TREHALASE 20 458 1.5E-183
8 g17178.t18 PRINTS PR00744 Glycosyl hydrolase family 37 signature 110 128 3.2E-46
10 g17178.t18 PRINTS PR00744 Glycosyl hydrolase family 37 signature 174 191 3.2E-46
7 g17178.t18 PRINTS PR00744 Glycosyl hydrolase family 37 signature 209 226 3.2E-46
4 g17178.t18 PRINTS PR00744 Glycosyl hydrolase family 37 signature 246 263 3.2E-46
9 g17178.t18 PRINTS PR00744 Glycosyl hydrolase family 37 signature 289 305 3.2E-46
5 g17178.t18 PRINTS PR00744 Glycosyl hydrolase family 37 signature 359 375 3.2E-46
6 g17178.t18 PRINTS PR00744 Glycosyl hydrolase family 37 signature 439 452 3.2E-46
1 g17178.t18 Pfam PF01204 Trehalase 16 456 8.0E-153
12 g17178.t18 ProSitePatterns PS00927 Trehalase signature 1. 68 81 -
13 g17178.t18 ProSitePatterns PS00928 Trehalase signature 2. 366 375 -
11 g17178.t18 SUPERFAMILY SSF48208 Six-hairpin glycosidases 17 456 9.83E-141

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:0004555 alpha,alpha-trehalase activity MF
GO:0005975 carbohydrate metabolic process BP
GO:0005991 trehalose 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