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.t6 TTS g17178.t6 12729498 12729498
chr_4 g17178 g17178.t6 isoform g17178.t6 12729651 12740216
chr_4 g17178 g17178.t6 exon g17178.t6.exon1 12729651 12729653
chr_4 g17178 g17178.t6 exon g17178.t6.exon2 12729715 12729800
chr_4 g17178 g17178.t6 cds g17178.t6.CDS1 12729721 12729800
chr_4 g17178 g17178.t6 exon g17178.t6.exon3 12730482 12730608
chr_4 g17178 g17178.t6 cds g17178.t6.CDS2 12730482 12730608
chr_4 g17178 g17178.t6 exon g17178.t6.exon4 12730787 12731185
chr_4 g17178 g17178.t6 cds g17178.t6.CDS3 12730787 12731185
chr_4 g17178 g17178.t6 exon g17178.t6.exon5 12731252 12731830
chr_4 g17178 g17178.t6 cds g17178.t6.CDS4 12731252 12731830
chr_4 g17178 g17178.t6 exon g17178.t6.exon6 12732419 12732642
chr_4 g17178 g17178.t6 cds g17178.t6.CDS5 12732419 12732642
chr_4 g17178 g17178.t6 exon g17178.t6.exon7 12732703 12732965
chr_4 g17178 g17178.t6 cds g17178.t6.CDS6 12732703 12732965
chr_4 g17178 g17178.t6 exon g17178.t6.exon8 12733078 12733273
chr_4 g17178 g17178.t6 cds g17178.t6.CDS7 12733078 12733202
chr_4 g17178 g17178.t6 exon g17178.t6.exon9 12740147 12740216
chr_4 g17178 g17178.t6 TSS g17178.t6 12740216 12740216

Sequences

>g17178.t6 Gene=g17178 Length=1947
GTTTGTTCATAAGCCGCGGTTGAGTGAGACACGAAAAGACGACAGCAGTCGCGGTTTGCA
ATTTTTTTGTAATAAATTTAAGTATTAGTAAAAAAAGCCAAAATAAAGACAATCAAAAAA
GATTGAGTGAATTGTGATAAAATGTTTAACATTCTGAACTTCCTGTTAGTATTATTGTTA
ATCGATGTAGTTTATGTTAGTGCATTATTAATTTATCGTCGTTTTGAAGACGAAGATATC
CGTCAATATCCACCACCATGCCCGAGCGAAGTCTACTGTCATGGAAATTTATTACACACA
GTACAGATGGCTCGACTTTATAATGATTCAAAGACTTTTGTTGATATGAAACTCAAAAAT
CCACCACATGAGACTATACAGCTTTTTAATAATTTTATGGCTGATTTTCCTGATGGTTTA
CCCGACACTGATAAACTTCGACAATGGGTTGAAGAACATTTTGATGAACCTGGTTCTGAA
TTTGAGCAATGGACGCCCGATGATTTTCAAAAATCACCAAAATTCTTAGATAAAATAAGT
GATAAAAACTTCCGTGATTTTGCAAGTGAATTAAATGGAATTTGGTTAGAATTGGGAAGA
AAAATGAAGCCAGATGTAAAAATTAATGAAGATCACTATTCAATAATTCATGTCGATAAT
CCAGTAATTGTGCCAGGTGGAAGATTTAGAGAATTCTATTATTGGGATTCTTATTGGGTC
ATTCGAGGTTTACTGCTGTGTGAAATGTACAATACAACAAAAGGAATGCTTGAAAATTTC
ATGTCAATAGTAACACGTTACGGTTTTATTCCAAATGGTGGCAGAATATATTATTCGTTA
CGTTCTCAGCCGCCACTTCTTGCACCAATGGTCAAAACTTATGTTGAAACCACAAATGAT
ATTGATTTTGCTGTAAAATATGTTGATGTACTTGCATTAGAATTTAATTATTGGTTGGCA
AATCACACAGTACAAGTTAAAGGACACACATTAGCAAGATATGGTGATAAATCAAATGGA
CCAAGACCAGAAAGTTATAGAGAAGATATAGAAACAGGAAGTGGTTTTCAAAGTGCAAAG
GACAAAGAAGAACATTATGCAGAATTGAAAGCAGCTGCTGAAAGTGGAATGGACTTTTCA
TCGCGATGGTTTATCAATGATGAAGGCACAAATGTTGGAACACTTGAGAATTTAAAGACA
AGATATATCATACCAGTTGAATTAAATGCTATTTTATATTGGAATGCCGTCATTATTGCT
GAATTTTATGCTATTGCTGGCAATGAAACTAGAAAAAAAGAATACCTTAGAATAGCTAAG
GACTTTATGGATGCTGTAAATGAAGTGTTATGGGATGAAGAAACTGGAGCATGGCTCGAT
TATGATCTGATAAATGAAAAACACAGAAATTATTTCGTTCCAACAAATCTTTCGCCACTT
TGGATGAAATGCTATGATATAACAAAACGCGAACACATTGCCTCAAAAGTCTTACAGTAT
ATTGATAATTTAAAACTTGATGATTATCCTGGTGGTGTTCCAACAACTCTCATGAACAGT
GGTGAACAATGGGATTGGCCAAATGTATGGGCACCAACGCAACATATTTTAATTGTTGGA
TTAGAAAATCTTGGTGTTAAAGAGGCTCAAGAAAAAGCACAAGATTATGCACAACGATGG
GTGCATGGCAATTATATTGCATTCAAAGAGAGTGGAGCTATGTATGAAAAGTATCTTGCA
ACAGAACTCGGCGGACATGGTGGAGGTGGTGAATATGAAGTCCAAAAAGGCTTCGGATGG
ACAAATGGTGTAATTCTTGATCTCCTTGATCGTTATGGCGAAGTTTTAAGTTCTTCAGTT
AAACCATCAACATTAGGAAAATTATTTACTGGAATAATTGCAGTGTCATCAATAATGATT
TCTAGAGTTAGCTGGTGAGAAATGACT

>g17178.t6 Gene=g17178 Length=598
MFNILNFLLVLLLIDVVYVSALLIYRRFEDEDIRQYPPPCPSEVYCHGNLLHTVQMARLY
NDSKTFVDMKLKNPPHETIQLFNNFMADFPDGLPDTDKLRQWVEEHFDEPGSEFEQWTPD
DFQKSPKFLDKISDKNFRDFASELNGIWLELGRKMKPDVKINEDHYSIIHVDNPVIVPGG
RFREFYYWDSYWVIRGLLLCEMYNTTKGMLENFMSIVTRYGFIPNGGRIYYSLRSQPPLL
APMVKTYVETTNDIDFAVKYVDVLALEFNYWLANHTVQVKGHTLARYGDKSNGPRPESYR
EDIETGSGFQSAKDKEEHYAELKAAAESGMDFSSRWFINDEGTNVGTLENLKTRYIIPVE
LNAILYWNAVIIAEFYAIAGNETRKKEYLRIAKDFMDAVNEVLWDEETGAWLDYDLINEK
HRNYFVPTNLSPLWMKCYDITKREHIASKVLQYIDNLKLDDYPGGVPTTLMNSGEQWDWP
NVWAPTQHILIVGLENLGVKEAQEKAQDYAQRWVHGNYIAFKESGAMYEKYLATELGGHG
GGGEYEVQKGFGWTNGVILDLLDRYGEVLSSSVKPSTLGKLFTGIIAVSSIMISRVSW

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g17178.t6 Gene3D G3DSA:1.50.10.10 - 36 577 2.5E-194
2 g17178.t6 PANTHER PTHR23403 TREHALASE 37 567 5.9E-217
3 g17178.t6 PANTHER PTHR23403:SF1 TREHALASE 37 567 5.9E-217
7 g17178.t6 PRINTS PR00744 Glycosyl hydrolase family 37 signature 220 238 1.4E-45
5 g17178.t6 PRINTS PR00744 Glycosyl hydrolase family 37 signature 284 301 1.4E-45
4 g17178.t6 PRINTS PR00744 Glycosyl hydrolase family 37 signature 319 336 1.4E-45
9 g17178.t6 PRINTS PR00744 Glycosyl hydrolase family 37 signature 356 373 1.4E-45
10 g17178.t6 PRINTS PR00744 Glycosyl hydrolase family 37 signature 399 415 1.4E-45
6 g17178.t6 PRINTS PR00744 Glycosyl hydrolase family 37 signature 469 485 1.4E-45
8 g17178.t6 PRINTS PR00744 Glycosyl hydrolase family 37 signature 549 562 1.4E-45
1 g17178.t6 Pfam PF01204 Trehalase 59 566 4.7E-167
15 g17178.t6 Phobius SIGNAL_PEPTIDE Signal peptide region 1 21 -
16 g17178.t6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
17 g17178.t6 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 14 -
18 g17178.t6 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 21 -
14 g17178.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 22 598 -
20 g17178.t6 ProSitePatterns PS00927 Trehalase signature 1. 178 191 -
21 g17178.t6 ProSitePatterns PS00928 Trehalase signature 2. 476 485 -
11 g17178.t6 SUPERFAMILY SSF48208 Six-hairpin glycosidases 40 566 5.29E-157
12 g17178.t6 SignalP_EUK SignalP-TM SignalP-TM 1 21 -
19 g17178.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 2 24 -

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