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.t1 TTS g17178.t1 12729498 12729498
chr_4 g17178 g17178.t1 isoform g17178.t1 12729721 12745419
chr_4 g17178 g17178.t1 exon g17178.t1.exon1 12729721 12729800
chr_4 g17178 g17178.t1 cds g17178.t1.CDS1 12729721 12729800
chr_4 g17178 g17178.t1 exon g17178.t1.exon2 12730482 12730608
chr_4 g17178 g17178.t1 cds g17178.t1.CDS2 12730482 12730608
chr_4 g17178 g17178.t1 exon g17178.t1.exon3 12730787 12731185
chr_4 g17178 g17178.t1 cds g17178.t1.CDS3 12730787 12731185
chr_4 g17178 g17178.t1 exon g17178.t1.exon4 12731252 12731830
chr_4 g17178 g17178.t1 cds g17178.t1.CDS4 12731252 12731830
chr_4 g17178 g17178.t1 exon g17178.t1.exon5 12732419 12732642
chr_4 g17178 g17178.t1 cds g17178.t1.CDS5 12732419 12732642
chr_4 g17178 g17178.t1 exon g17178.t1.exon6 12732703 12732965
chr_4 g17178 g17178.t1 cds g17178.t1.CDS6 12732703 12732965
chr_4 g17178 g17178.t1 exon g17178.t1.exon7 12733461 12733505
chr_4 g17178 g17178.t1 cds g17178.t1.CDS7 12733461 12733505
chr_4 g17178 g17178.t1 exon g17178.t1.exon8 12745400 12745419
chr_4 g17178 g17178.t1 cds g17178.t1.CDS8 12745400 12745419
chr_4 g17178 g17178.t1 TSS g17178.t1 12745583 12745583

Sequences

>g17178.t1 Gene=g17178 Length=1737
ATGCCTTCTGAGGAAAGCAGTCACAATGATGTATATTATCATCCAACTGCTGTTGGTAGT
AATGGCGAAGTCTACTGTCATGGAAATTTATTACACACAGTACAGATGGCTCGACTTTAT
AATGATTCAAAGACTTTTGTTGATATGAAACTCAAAAATCCACCACATGAGACTATACAG
CTTTTTAATAATTTTATGGCTGATTTTCCTGATGGTTTACCCGACACTGATAAACTTCGA
CAATGGGTTGAAGAACATTTTGATGAACCTGGTTCTGAATTTGAGCAATGGACGCCCGAT
GATTTTCAAAAATCACCAAAATTCTTAGATAAAATAAGTGATAAAAACTTCCGTGATTTT
GCAAGTGAATTAAATGGAATTTGGTTAGAATTGGGAAGAAAAATGAAGCCAGATGTAAAA
ATTAATGAAGATCACTATTCAATAATTCATGTCGATAATCCAGTAATTGTGCCAGGTGGA
AGATTTAGAGAATTCTATTATTGGGATTCTTATTGGGTCATTCGAGGTTTACTGCTGTGT
GAAATGTACAATACAACAAAAGGAATGCTTGAAAATTTCATGTCAATAGTAACACGTTAC
GGTTTTATTCCAAATGGTGGCAGAATATATTATTCGTTACGTTCTCAGCCGCCACTTCTT
GCACCAATGGTCAAAACTTATGTTGAAACCACAAATGATATTGATTTTGCTGTAAAATAT
GTTGATGTACTTGCATTAGAATTTAATTATTGGTTGGCAAATCACACAGTACAAGTTAAA
GGACACACATTAGCAAGATATGGTGATAAATCAAATGGACCAAGACCAGAAAGTTATAGA
GAAGATATAGAAACAGGAAGTGGTTTTCAAAGTGCAAAGGACAAAGAAGAACATTATGCA
GAATTGAAAGCAGCTGCTGAAAGTGGAATGGACTTTTCATCGCGATGGTTTATCAATGAT
GAAGGCACAAATGTTGGAACACTTGAGAATTTAAAGACAAGATATATCATACCAGTTGAA
TTAAATGCTATTTTATATTGGAATGCCGTCATTATTGCTGAATTTTATGCTATTGCTGGC
AATGAAACTAGAAAAAAAGAATACCTTAGAATAGCTAAGGACTTTATGGATGCTGTAAAT
GAAGTGTTATGGGATGAAGAAACTGGAGCATGGCTCGATTATGATCTGATAAATGAAAAA
CACAGAAATTATTTCGTTCCAACAAATCTTTCGCCACTTTGGATGAAATGCTATGATATA
ACAAAACGCGAACACATTGCCTCAAAAGTCTTACAGTATATTGATAATTTAAAACTTGAT
GATTATCCTGGTGGTGTTCCAACAACTCTCATGAACAGTGGTGAACAATGGGATTGGCCA
AATGTATGGGCACCAACGCAACATATTTTAATTGTTGGATTAGAAAATCTTGGTGTTAAA
GAGGCTCAAGAAAAAGCACAAGATTATGCACAACGATGGGTGCATGGCAATTATATTGCA
TTCAAAGAGAGTGGAGCTATGTATGAAAAGTATCTTGCAACAGAACTCGGCGGACATGGT
GGAGGTGGTGAATATGAAGTCCAAAAAGGCTTCGGATGGACAAATGGTGTAATTCTTGAT
CTCCTTGATCGTTATGGCGAAGTTTTAAGTTCTTCAGTTAAACCATCAACATTAGGAAAA
TTATTTACTGGAATAATTGCAGTGTCATCAATAATGATTTCTAGAGTTAGCTGGTGA

>g17178.t1 Gene=g17178 Length=578
MPSEESSHNDVYYHPTAVGSNGEVYCHGNLLHTVQMARLYNDSKTFVDMKLKNPPHETIQ
LFNNFMADFPDGLPDTDKLRQWVEEHFDEPGSEFEQWTPDDFQKSPKFLDKISDKNFRDF
ASELNGIWLELGRKMKPDVKINEDHYSIIHVDNPVIVPGGRFREFYYWDSYWVIRGLLLC
EMYNTTKGMLENFMSIVTRYGFIPNGGRIYYSLRSQPPLLAPMVKTYVETTNDIDFAVKY
VDVLALEFNYWLANHTVQVKGHTLARYGDKSNGPRPESYREDIETGSGFQSAKDKEEHYA
ELKAAAESGMDFSSRWFINDEGTNVGTLENLKTRYIIPVELNAILYWNAVIIAEFYAIAG
NETRKKEYLRIAKDFMDAVNEVLWDEETGAWLDYDLINEKHRNYFVPTNLSPLWMKCYDI
TKREHIASKVLQYIDNLKLDDYPGGVPTTLMNSGEQWDWPNVWAPTQHILIVGLENLGVK
EAQEKAQDYAQRWVHGNYIAFKESGAMYEKYLATELGGHGGGGEYEVQKGFGWTNGVILD
LLDRYGEVLSSSVKPSTLGKLFTGIIAVSSIMISRVSW

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g17178.t1 Gene3D G3DSA:1.50.10.10 - 16 557 7.1E-194
2 g17178.t1 PANTHER PTHR23403 TREHALASE 19 547 2.9E-216
3 g17178.t1 PANTHER PTHR23403:SF1 TREHALASE 19 547 2.9E-216
6 g17178.t1 PRINTS PR00744 Glycosyl hydrolase family 37 signature 200 218 1.1E-45
5 g17178.t1 PRINTS PR00744 Glycosyl hydrolase family 37 signature 264 281 1.1E-45
10 g17178.t1 PRINTS PR00744 Glycosyl hydrolase family 37 signature 299 316 1.1E-45
9 g17178.t1 PRINTS PR00744 Glycosyl hydrolase family 37 signature 336 353 1.1E-45
4 g17178.t1 PRINTS PR00744 Glycosyl hydrolase family 37 signature 379 395 1.1E-45
8 g17178.t1 PRINTS PR00744 Glycosyl hydrolase family 37 signature 449 465 1.1E-45
7 g17178.t1 PRINTS PR00744 Glycosyl hydrolase family 37 signature 529 542 1.1E-45
1 g17178.t1 Pfam PF01204 Trehalase 39 546 4.2E-167
12 g17178.t1 ProSitePatterns PS00927 Trehalase signature 1. 158 171 -
13 g17178.t1 ProSitePatterns PS00928 Trehalase signature 2. 456 465 -
11 g17178.t1 SUPERFAMILY SSF48208 Six-hairpin glycosidases 24 546 5.67E-156

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