General information for g4375.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Glycogen debranching enzyme.
Parent gene
- The parent gene g4375 is located on chr_2: 1725663..1726416 (+ 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_2 | g4375 | g4375.t3 | isoform | g4375.t3 | 1722358 | 1723098 |
| chr_2 | g4375 | g4375.t3 | exon | g4375.t3.exon1 | 1722358 | 1723098 |
| chr_2 | g4375 | g4375.t3 | cds | g4375.t3.CDS1 | 1722358 | 1723098 |
| chr_2 | g4375 | g4375.t3 | TSS | g4375.t3 | NA | NA |
| chr_2 | g4375 | g4375.t3 | TTS | g4375.t3 | NA | NA |
Sequences
>g4375.t3 Gene=g4375 Length=741
ATGAGAACACGTGCACCACCAACTGCTTTAACAGAAGCTGTTTCAACTGAACTTACGTTT
GAAACACCAATCAATTATACTCGAAAAGAGGTTCATATAAACATAGAACATGCTTTGAAA
ATTTATAATGTCTTTAGACCAGATTGTTTCGATGAAGACACTCGTGTACGAAGATGTGGT
GAAACTTTCCGTAAAGTACTCGAGGATTATAATAATAAAATTCGAGCAGAAATAGATGGA
ATGATGAACTATGCAATTGACAATTGTATTGCAGGAGCACGCTATGAAAGAGTTCAAAAT
GACGGTCCAAAATACAGAACGATTGATGTTTCACATCCATTATTTGTGCCATATTTTACT
CATACCAATGCAGAAAAGGCCACAATTGAAGAGGTTGAAAAAATGATGTATGGAGAAGGT
GGAAAATATTTTATGGGTCATAATGGATGGGTTTTGGGCCAAGATGCTCTAGTTGATTTT
GCTCTTAAACAAGCTGGCATTGGTAATGTTTATTTGAAAAGAGAGATTATCGCTTGGGGA
GATTCTGTAAAACTTAGATATGGTGAGAAGCCTGAAGATAGTCCATATTTATGGCAACGT
ATGAAAGAATATGTCGAAACAACTGCTAAATATTTTGATGGACTTCGTCTCGACAACTGC
CATTCGACTCCTTTACATGTGGCAGAATATTTGATTGATTGTGCACGAAAGGTCAATCCG
GAGCTCTATGTTGTTGCAGAA
>g4375.t3 Gene=g4375 Length=247
MRTRAPPTALTEAVSTELTFETPINYTRKEVHINIEHALKIYNVFRPDCFDEDTRVRRCG
ETFRKVLEDYNNKIRAEIDGMMNYAIDNCIAGARYERVQNDGPKYRTIDVSHPLFVPYFT
HTNAEKATIEEVEKMMYGEGGKYFMGHNGWVLGQDALVDFALKQAGIGNVYLKREIIAWG
DSVKLRYGEKPEDSPYLWQRMKEYVETTAKYFDGLRLDNCHSTPLHVAEYLIDCARKVNP
ELYVVAE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g4375.t3 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 145 | 247 | 1e-07 |
| 2 | g4375.t3 | PANTHER | PTHR10569 | GLYCOGEN DEBRANCHING ENZYME | 16 | 247 | 0e+00 |
| 1 | g4375.t3 | Pfam | PF14701 | Glycogen debranching enzyme, glucanotransferase domain | 18 | 243 | 0e+00 |
| 3 | g4375.t3 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 138 | 247 | 0e+00 |
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:0004135 | amylo-alpha-1,6-glucosidase activity | MF |
| GO:0005980 | glycogen catabolic process | BP |
| GO:0004134 | 4-alpha-glucanotransferase activity | MF |
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.
