Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Glucosidase 2 subunit beta.

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 g1963 g1963.t4 TSS g1963.t4 14109864 14109864
chr_3 g1963 g1963.t4 isoform g1963.t4 14109993 14110967
chr_3 g1963 g1963.t4 exon g1963.t4.exon1 14109993 14110074
chr_3 g1963 g1963.t4 cds g1963.t4.CDS1 14109993 14110074
chr_3 g1963 g1963.t4 exon g1963.t4.exon2 14110175 14110270
chr_3 g1963 g1963.t4 cds g1963.t4.CDS2 14110175 14110270
chr_3 g1963 g1963.t4 exon g1963.t4.exon3 14110343 14110967
chr_3 g1963 g1963.t4 cds g1963.t4.CDS3 14110343 14110965
chr_3 g1963 g1963.t4 TTS g1963.t4 14111869 14111869

Sequences

>g1963.t4 Gene=g1963 Length=803
ATGATTGTGAATTTACCAATTTTAAGTATTGTAATAGGAATTTTTAGCTATTTTGCGTTA
TGTGATAAACCAATTTTGAGAGGTATTGATCCTCAAAGAGCTCAATTATATGCAAATAAC
AATGACAAATTTACTTGTTTCGATGGGAAAAAGACGATAAAGTACACGCAGCTGAATGAT
GACTATTGTGATTGTGCTGATGCAAGCGATGAGCCAGGCACTTCTGCGTGTGTTAGTGGA
AGATTTTTCTGTATCAATGCCGGTTTTAAGAGTTTAATAATTCCAAGTTCTCGTGTAAAT
GATGGAATTTGTGATTGTTGCGATGGTTCAGATGAATACTTTAGTAACGCAAAATGTATA
AATAATTGCATTGAACTCGGATCAGCTGATCGATTGAGAGAAAAGCAGCTAGCAGAATTA
CTAAAGAATGGCAATCAACTTAGACTAGAATTAGCTCAGAAAGGAAAGAAATTAAAAGAA
GATCAGAAGATAAGGTTGGCAGAATTAGAAAAATCAAAAGATCAAGCCAACAAAATACGA
GAAGAAAAAAGACAAATTAAGGCAGATGCCGAAATTTTCGAAAATGATGCTTTGAATGTT
TATCGACAAGCAGAAGAAGAGAGTAAAAAGCAAAAGGAAGAAGAAGAAGCTCAAAAGAAT
CGAGTTGAAGCTGAAGAGACTTTTCTTAAATACGATTCAAATAGCGATGGAAAAGTCGAC
ATTACTGAGCTACAAACAAGAATTGTTTTTGATAAAAATCGCAATGGAATAGTTGAAATA
GAAGAAGCTCGATATTTCTTAGA

>g1963.t4 Gene=g1963 Length=267
MIVNLPILSIVIGIFSYFALCDKPILRGIDPQRAQLYANNNDKFTCFDGKKTIKYTQLND
DYCDCADASDEPGTSACVSGRFFCINAGFKSLIIPSSRVNDGICDCCDGSDEYFSNAKCI
NNCIELGSADRLREKQLAELLKNGNQLRLELAQKGKKLKEDQKIRLAELEKSKDQANKIR
EEKRQIKADAEIFENDALNVYRQAEEESKKQKEEEEAQKNRVEAEETFLKYDSNSDGKVD
ITELQTRIVFDKNRNGIVEIEEARYFL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g1963.t4 Coils Coil Coil 159 227 -
6 g1963.t4 Gene3D G3DSA:4.10.400.10 - 37 120 4.6E-5
3 g1963.t4 PANTHER PTHR12630:SF1 GLUCOSIDASE 2 SUBUNIT BETA 22 246 5.3E-64
4 g1963.t4 PANTHER PTHR12630 N-LINKED OLIGOSACCHARIDE PROCESSING 22 246 5.3E-64
2 g1963.t4 Pfam PF12999 Glucosidase II beta subunit-like 22 173 2.2E-40
1 g1963.t4 Pfam PF13202 EF hand 226 246 2.6E-4
9 g1963.t4 Phobius SIGNAL_PEPTIDE Signal peptide region 1 21 -
10 g1963.t4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 4 -
11 g1963.t4 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 5 16 -
12 g1963.t4 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 17 21 -
8 g1963.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 22 267 -
13 g1963.t4 ProSitePatterns PS00018 EF-hand calcium-binding domain. 232 244 -
14 g1963.t4 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 219 254 9.325
5 g1963.t4 SUPERFAMILY SSF47473 EF-hand 217 262 8.07E-6

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:0005515 protein binding MF
GO:0005509 calcium ion binding MF
GO:0006491 N-glycan processing 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