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.t29 TTS g17178.t29 12730043 12730043
chr_4 g17178 g17178.t29 isoform g17178.t29 12731022 12740216
chr_4 g17178 g17178.t29 exon g17178.t29.exon1 12731022 12731185
chr_4 g17178 g17178.t29 cds g17178.t29.CDS1 12731024 12731185
chr_4 g17178 g17178.t29 exon g17178.t29.exon2 12731252 12731830
chr_4 g17178 g17178.t29 cds g17178.t29.CDS2 12731252 12731830
chr_4 g17178 g17178.t29 exon g17178.t29.exon3 12732419 12732642
chr_4 g17178 g17178.t29 cds g17178.t29.CDS3 12732419 12732642
chr_4 g17178 g17178.t29 exon g17178.t29.exon4 12732703 12732965
chr_4 g17178 g17178.t29 cds g17178.t29.CDS4 12732703 12732965
chr_4 g17178 g17178.t29 exon g17178.t29.exon5 12733078 12733273
chr_4 g17178 g17178.t29 cds g17178.t29.CDS5 12733078 12733202
chr_4 g17178 g17178.t29 exon g17178.t29.exon6 12740149 12740216
chr_4 g17178 g17178.t29 TSS g17178.t29 12740216 12740216

Sequences

>g17178.t29 Gene=g17178 Length=1494
GTTTGTTCATAAGCCGCGGTTGAGTGAGACACGAAAAGACGACAGCAGTCGCGGTTTGCA
ATTTTTTTAATAAATTTAAGTATTAGTAAAAAAAGCCAAAATAAAGACAATCAAAAAAGA
TTGAGTGAATTGTGATAAAATGTTTAACATTCTGAACTTCCTGTTAGTATTATTGTTAAT
CGATGTAGTTTATGTTAGTGCATTATTAATTTATCGTCGTTTTGAAGACGAAGATATCCG
TCAATATCCACCACCATGCCCGAGCGAAGTCTACTGTCATGGAAATTTATTACACACAGT
ACAGATGGCTCGACTTTATAATGATTCAAAGACTTTTGTTGATATGAAACTCAAAAATCC
ACCACATGAGACTATACAGCTTTTTAATAATTTTATGGCTGATTTTCCTGATGGTTTACC
CGACACTGATAAACTTCGACAATGGGTTGAAGAACATTTTGATGAACCTGGTTCTGAATT
TGAGCAATGGACGCCCGATGATTTTCAAAAATCACCAAAATTCTTAGATAAAATAAGTGA
TAAAAACTTCCGTGATTTTGCAAGTGAATTAAATGGAATTTGGTTAGAATTGGGAAGAAA
AATGAAGCCAGATGTAAAAATTAATGAAGATCACTATTCAATAATTCATGTCGATAATCC
AGTAATTGTGCCAGGTGGAAGATTTAGAGAATTCTATTATTGGGATTCTTATTGGGTCAT
TCGAGGTTTACTGCTGTGTGAAATGTACAATACAACAAAAGGAATGCTTGAAAATTTCAT
GTCAATAGTAACACGTTACGGTTTTATTCCAAATGGTGGCAGAATATATTATTCGTTACG
TTCTCAGCCGCCACTTCTTGCACCAATGGTCAAAACTTATGTTGAAACCACAAATGATAT
TGATTTTGCTGTAAAATATGTTGATGTACTTGCATTAGAATTTAATTATTGGTTGGCAAA
TCACACAGTACAAGTTAAAGGACACACATTAGCAAGATATGGTGATAAATCAAATGGACC
AAGACCAGAAAGTTATAGAGAAGATATAGAAACAGGAAGTGGTTTTCAAAGTGCAAAGGA
CAAAGAAGAACATTATGCAGAATTGAAAGCAGCTGCTGAAAGTGGAATGGACTTTTCATC
GCGATGGTTTATCAATGATGAAGGCACAAATGTTGGAACACTTGAGAATTTAAAGACAAG
ATATATCATACCAGTTGAATTAAATGCTATTTTATATTGGAATGCCGTCATTATTGCTGA
ATTTTATGCTATTGCTGGCAATGAAACTAGAAAAAAAGAATACCTTAGAATAGCTAAGGA
CTTTATGGATGCTGTAAATGAAGTGTTATGGGATGAAGAAACTGGAGCATGGCTCGATTA
TGATCTGATAAATGAAAAACACAGAAATTATTTCGTTCCAACAAATCTTTCGCCACTTTG
GATGAAATGCTATGATATAACAAAACGCGAACACATTGCCTCAAAAGTCTTACA

>g17178.t29 Gene=g17178 Length=451
MFNILNFLLVLLLIDVVYVSALLIYRRFEDEDIRQYPPPCPSEVYCHGNLLHTVQMARLY
NDSKTFVDMKLKNPPHETIQLFNNFMADFPDGLPDTDKLRQWVEEHFDEPGSEFEQWTPD
DFQKSPKFLDKISDKNFRDFASELNGIWLELGRKMKPDVKINEDHYSIIHVDNPVIVPGG
RFREFYYWDSYWVIRGLLLCEMYNTTKGMLENFMSIVTRYGFIPNGGRIYYSLRSQPPLL
APMVKTYVETTNDIDFAVKYVDVLALEFNYWLANHTVQVKGHTLARYGDKSNGPRPESYR
EDIETGSGFQSAKDKEEHYAELKAAAESGMDFSSRWFINDEGTNVGTLENLKTRYIIPVE
LNAILYWNAVIIAEFYAIAGNETRKKEYLRIAKDFMDAVNEVLWDEETGAWLDYDLINEK
HRNYFVPTNLSPLWMKCYDITKREHIASKVL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g17178.t29 Gene3D G3DSA:1.50.10.10 - 36 451 1.0E-147
2 g17178.t29 PANTHER PTHR23403 TREHALASE 37 444 5.0E-164
3 g17178.t29 PANTHER PTHR23403:SF1 TREHALASE 37 444 5.0E-164
6 g17178.t29 PRINTS PR00744 Glycosyl hydrolase family 37 signature 220 238 7.2E-34
5 g17178.t29 PRINTS PR00744 Glycosyl hydrolase family 37 signature 284 301 7.2E-34
4 g17178.t29 PRINTS PR00744 Glycosyl hydrolase family 37 signature 319 336 7.2E-34
7 g17178.t29 PRINTS PR00744 Glycosyl hydrolase family 37 signature 356 373 7.2E-34
8 g17178.t29 PRINTS PR00744 Glycosyl hydrolase family 37 signature 399 415 7.2E-34
1 g17178.t29 Pfam PF01204 Trehalase 59 450 3.0E-122
13 g17178.t29 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
14 g17178.t29 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 25 -
12 g17178.t29 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 26 451 -
16 g17178.t29 ProSitePatterns PS00927 Trehalase signature 1. 178 191 -
9 g17178.t29 SUPERFAMILY SSF48208 Six-hairpin glycosidases 40 448 6.8E-117
10 g17178.t29 SignalP_EUK SignalP-TM SignalP-TM 1 21 -
15 g17178.t29 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

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.

Raw TPM values