General information for g1963.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Glucosidase 2 subunit beta.
Parent gene
- The parent gene g1963 is located on chr_3: 14111583..14111817 (+ strand)
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.t1 | TSS | g1963.t1 | 14109864 | 14109864 |
| chr_3 | g1963 | g1963.t1 | isoform | g1963.t1 | 14109993 | 14111817 |
| chr_3 | g1963 | g1963.t1 | exon | g1963.t1.exon1 | 14109993 | 14110074 |
| chr_3 | g1963 | g1963.t1 | cds | g1963.t1.CDS1 | 14109993 | 14110074 |
| chr_3 | g1963 | g1963.t1 | exon | g1963.t1.exon2 | 14110175 | 14110270 |
| chr_3 | g1963 | g1963.t1 | cds | g1963.t1.CDS2 | 14110175 | 14110270 |
| chr_3 | g1963 | g1963.t1 | exon | g1963.t1.exon3 | 14110343 | 14111516 |
| chr_3 | g1963 | g1963.t1 | cds | g1963.t1.CDS3 | 14110343 | 14111516 |
| chr_3 | g1963 | g1963.t1 | exon | g1963.t1.exon4 | 14111586 | 14111817 |
| chr_3 | g1963 | g1963.t1 | cds | g1963.t1.CDS4 | 14111586 | 14111817 |
| chr_3 | g1963 | g1963.t1 | TTS | g1963.t1 | 14111869 | 14111869 |
Sequences
>g1963.t1 Gene=g1963 Length=1584
ATGATTGTGAATTTACCAATTTTAAGTATTGTAATAGGAATTTTTAGCTATTTTGCGTTA
TGTGATAAACCAATTTTGAGAGGTATTGATCCTCAAAGAGCTCAATTATATGCAAATAAC
AATGACAAATTTACTTGTTTCGATGGGAAAAAGACGATAAAGTACACGCAGCTGAATGAT
GACTATTGTGATTGTGCTGATGCAAGCGATGAGCCAGGCACTTCTGCGTGTGTTAGTGGA
AGATTTTTCTGTATCAATGCCGGTTTTAAGAGTTTAATAATTCCAAGTTCTCGTGTAAAT
GATGGAATTTGTGATTGTTGCGATGGTTCAGATGAATACTTTAGTAACGCAAAATGTATA
AATAATTGCATTGAACTCGGATCAGCTGATCGATTGAGAGAAAAGCAGCTAGCAGAATTA
CTAAAGAATGGCAATCAACTTAGACTAGAATTAGCTCAGAAAGGAAAGAAATTAAAAGAA
GATCAGAAGATAAGGTTGGCAGAATTAGAAAAATCAAAAGATCAAGCCAACAAAATACGA
GAAGAAAAAAGACAAATTAAGGCAGATGCCGAAATTTTCGAAAATGATGCTTTGAATGTT
TATCGACAAGCAGAAGAAGAGAGTAAAAAGCAAAAGGAAGAAGAAGAAGCTCAAAAGAAT
CGAGTTGAAGCTGAAGAGACTTTTCTTAAATACGATTCAAATAGCGATGGAAAAGTCGAC
ATTACTGAGCTACAAACAAGAATTGTTTTTGATAAAAATCGCAATGGAATAGTTGAAATA
GAAGAAGCTCGATATTTCTTAGACGACAATGATGAACTCGATTTAGAGAGTTTCATTACA
CTCGGATGGCCAAAGATTAAACCATTCCTCATGCTTGACTCAGGATTGTTCAAACCTCCA
AGAAGAAACGATGAACCAATTGATGATGAGGAGGAAGAACATGAGGTAGAACAACAAGGA
GGAGAGGAACCAAATGAGGAAGCAGAACTATTGAATGAAGAAGAGGAACAACATCATGAA
GAAGAAGGTGAATTTGATGAGGAAGCACAAGAAGAGCCACAAAATGAGGCACCGCCAACA
CCTCAAGTTCAATATGATGATGAAACACAAAGATTAATTCATGAAGCCAATGAAGCAAGA
AATCAATATGACATCGCTGATCGTGAATATAGAGAAATTGAAACAGAATTTAATAAGATT
AAGAGTGCACTTGAAAAAGACTTTGGTCCTGAGGAAGAATTTGCACCACTCAATGGTGAA
TGCTTCAATTATGAAGATCGTGAATACATTTATAAATTGTGCATGTTTGACAAGGCTACA
CAACAGCCTAAATCAGGTGGAAGCGAAACTAGACTGGGTGGTTGGGATGGTTGGAAAAGT
AACGATTACCGACAAATGTTTTATTCAAATGGTGCAGGCTGTTGGAATGGCCCGTCACGT
TCAACATTGGTCGATATAGAATGTGGTTTAGATACGAGAATTTTAAGTGTCACAGAGCCA
AATAGATGTGAATACAATTTCAAAATTCAAACTCCAGCAGCTTGTTTTGCGGCATTGAGT
GCTGACACTCACGATGAGCTATAA
>g1963.t1 Gene=g1963 Length=527
MIVNLPILSIVIGIFSYFALCDKPILRGIDPQRAQLYANNNDKFTCFDGKKTIKYTQLND
DYCDCADASDEPGTSACVSGRFFCINAGFKSLIIPSSRVNDGICDCCDGSDEYFSNAKCI
NNCIELGSADRLREKQLAELLKNGNQLRLELAQKGKKLKEDQKIRLAELEKSKDQANKIR
EEKRQIKADAEIFENDALNVYRQAEEESKKQKEEEEAQKNRVEAEETFLKYDSNSDGKVD
ITELQTRIVFDKNRNGIVEIEEARYFLDDNDELDLESFITLGWPKIKPFLMLDSGLFKPP
RRNDEPIDDEEEEHEVEQQGGEEPNEEAELLNEEEEQHHEEEGEFDEEAQEEPQNEAPPT
PQVQYDDETQRLIHEANEARNQYDIADREYREIETEFNKIKSALEKDFGPEEEFAPLNGE
CFNYEDREYIYKLCMFDKATQQPKSGGSETRLGGWDGWKSNDYRQMFYSNGAGCWNGPSR
STLVDIECGLDTRILSVTEPNRCEYNFKIQTPAACFAALSADTHDEL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g1963.t1 | Coils | Coil | Coil | 159 | 227 | - |
| 10 | g1963.t1 | Coils | Coil | Coil | 331 | 351 | - |
| 9 | g1963.t1 | Coils | Coil | Coil | 369 | 396 | - |
| 8 | g1963.t1 | Gene3D | G3DSA:2.70.130.10 | - | 414 | 515 | 2.6E-27 |
| 19 | g1963.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 305 | 364 | - |
| 18 | g1963.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 308 | 353 | - |
| 4 | g1963.t1 | PANTHER | PTHR12630:SF1 | GLUCOSIDASE 2 SUBUNIT BETA | 22 | 517 | 3.7E-122 |
| 5 | g1963.t1 | PANTHER | PTHR12630 | N-LINKED OLIGOSACCHARIDE PROCESSING | 22 | 517 | 3.7E-122 |
| 3 | g1963.t1 | Pfam | PF12999 | Glucosidase II beta subunit-like | 22 | 173 | 1.0E-39 |
| 2 | g1963.t1 | Pfam | PF13202 | EF hand | 226 | 246 | 6.0E-4 |
| 1 | g1963.t1 | Pfam | PF13015 | Glucosidase II beta subunit-like protein | 381 | 516 | 2.6E-29 |
| 13 | g1963.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 21 | - |
| 14 | g1963.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 4 | - |
| 15 | g1963.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 5 | 16 | - |
| 16 | g1963.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 17 | 21 | - |
| 12 | g1963.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 22 | 527 | - |
| 17 | g1963.t1 | ProSitePatterns | PS00018 | EF-hand calcium-binding domain. | 232 | 244 | - |
| 20 | g1963.t1 | ProSiteProfiles | PS50222 | EF-hand calcium-binding domain profile. | 219 | 254 | 9.325 |
| 7 | g1963.t1 | SUPERFAMILY | SSF47473 | EF-hand | 221 | 280 | 5.15E-7 |
| 6 | g1963.t1 | SUPERFAMILY | SSF50911 | Mannose 6-phosphate receptor domain | 413 | 515 | 1.18E-17 |
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:0005509 | calcium ion binding | MF |
| GO:0006491 | N-glycan processing | BP |
KEGG
Orthology
- This transcript has been annotated with K08288 (protein kinase C substrate 80K-H)
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.
