General information for g1963.t6
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.t6 | TSS | g1963.t6 | 14109864 | 14109864 |
| chr_3 | g1963 | g1963.t6 | isoform | g1963.t6 | 14109993 | 14111817 |
| chr_3 | g1963 | g1963.t6 | exon | g1963.t6.exon1 | 14109993 | 14110074 |
| chr_3 | g1963 | g1963.t6 | exon | g1963.t6.exon2 | 14110179 | 14110270 |
| chr_3 | g1963 | g1963.t6 | exon | g1963.t6.exon3 | 14110343 | 14111516 |
| chr_3 | g1963 | g1963.t6 | cds | g1963.t6.CDS1 | 14111035 | 14111516 |
| chr_3 | g1963 | g1963.t6 | exon | g1963.t6.exon4 | 14111586 | 14111817 |
| chr_3 | g1963 | g1963.t6 | cds | g1963.t6.CDS2 | 14111586 | 14111817 |
| chr_3 | g1963 | g1963.t6 | TTS | g1963.t6 | 14111869 | 14111869 |
Sequences
>g1963.t6 Gene=g1963 Length=1580
ATGATTGTGAATTTACCAATTTTAAGTATTGTAATAGGAATTTTTAGCTATTTTGCGTTA
TGTGATAAACCAATTTTGAGAGTGATCCTCAAAGAGCTCAATTATATGCAAATAACAATG
ACAAATTTACTTGTTTCGATGGGAAAAAGACGATAAAGTACACGCAGCTGAATGATGACT
ATTGTGATTGTGCTGATGCAAGCGATGAGCCAGGCACTTCTGCGTGTGTTAGTGGAAGAT
TTTTCTGTATCAATGCCGGTTTTAAGAGTTTAATAATTCCAAGTTCTCGTGTAAATGATG
GAATTTGTGATTGTTGCGATGGTTCAGATGAATACTTTAGTAACGCAAAATGTATAAATA
ATTGCATTGAACTCGGATCAGCTGATCGATTGAGAGAAAAGCAGCTAGCAGAATTACTAA
AGAATGGCAATCAACTTAGACTAGAATTAGCTCAGAAAGGAAAGAAATTAAAAGAAGATC
AGAAGATAAGGTTGGCAGAATTAGAAAAATCAAAAGATCAAGCCAACAAAATACGAGAAG
AAAAAAGACAAATTAAGGCAGATGCCGAAATTTTCGAAAATGATGCTTTGAATGTTTATC
GACAAGCAGAAGAAGAGAGTAAAAAGCAAAAGGAAGAAGAAGAAGCTCAAAAGAATCGAG
TTGAAGCTGAAGAGACTTTTCTTAAATACGATTCAAATAGCGATGGAAAAGTCGACATTA
CTGAGCTACAAACAAGAATTGTTTTTGATAAAAATCGCAATGGAATAGTTGAAATAGAAG
AAGCTCGATATTTCTTAGACGACAATGATGAACTCGATTTAGAGAGTTTCATTACACTCG
GATGGCCAAAGATTAAACCATTCCTCATGCTTGACTCAGGATTGTTCAAACCTCCAAGAA
GAAACGATGAACCAATTGATGATGAGGAGGAAGAACATGAGGTAGAACAACAAGGAGGAG
AGGAACCAAATGAGGAAGCAGAACTATTGAATGAAGAAGAGGAACAACATCATGAAGAAG
AAGGTGAATTTGATGAGGAAGCACAAGAAGAGCCACAAAATGAGGCACCGCCAACACCTC
AAGTTCAATATGATGATGAAACACAAAGATTAATTCATGAAGCCAATGAAGCAAGAAATC
AATATGACATCGCTGATCGTGAATATAGAGAAATTGAAACAGAATTTAATAAGATTAAGA
GTGCACTTGAAAAAGACTTTGGTCCTGAGGAAGAATTTGCACCACTCAATGGTGAATGCT
TCAATTATGAAGATCGTGAATACATTTATAAATTGTGCATGTTTGACAAGGCTACACAAC
AGCCTAAATCAGGTGGAAGCGAAACTAGACTGGGTGGTTGGGATGGTTGGAAAAGTAACG
ATTACCGACAAATGTTTTATTCAAATGGTGCAGGCTGTTGGAATGGCCCGTCACGTTCAA
CATTGGTCGATATAGAATGTGGTTTAGATACGAGAATTTTAAGTGTCACAGAGCCAAATA
GATGTGAATACAATTTCAAAATTCAAACTCCAGCAGCTTGTTTTGCGGCATTGAGTGCTG
ACACTCACGATGAGCTATAA
>g1963.t6 Gene=g1963 Length=237
MLDSGLFKPPRRNDEPIDDEEEEHEVEQQGGEEPNEEAELLNEEEEQHHEEEGEFDEEAQ
EEPQNEAPPTPQVQYDDETQRLIHEANEARNQYDIADREYREIETEFNKIKSALEKDFGP
EEEFAPLNGECFNYEDREYIYKLCMFDKATQQPKSGGSETRLGGWDGWKSNDYRQMFYSN
GAGCWNGPSRSTLVDIECGLDTRILSVTEPNRCEYNFKIQTPAACFAALSADTHDEL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g1963.t6 | Coils | Coil | Coil | 41 | 61 | - |
| 9 | g1963.t6 | Coils | Coil | Coil | 79 | 106 | - |
| 7 | g1963.t6 | Gene3D | G3DSA:2.70.130.10 | - | 124 | 225 | 5.5E-28 |
| 6 | g1963.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 74 | - |
| 5 | g1963.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 18 | 63 | - |
| 2 | g1963.t6 | PANTHER | PTHR12630:SF1 | GLUCOSIDASE 2 SUBUNIT BETA | 20 | 227 | 2.1E-52 |
| 3 | g1963.t6 | PANTHER | PTHR12630 | N-LINKED OLIGOSACCHARIDE PROCESSING | 20 | 227 | 2.1E-52 |
| 1 | g1963.t6 | Pfam | PF13015 | Glucosidase II beta subunit-like protein | 91 | 226 | 4.1E-30 |
| 4 | g1963.t6 | SUPERFAMILY | SSF50911 | Mannose 6-phosphate receptor domain | 122 | 225 | 2.22E-18 |
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:0006491 | N-glycan processing | 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. There were no conditions that were differentially expressed