General information for g4375.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t6 | isoform | g4375.t6 | 1725324 | 1726223 |
| chr_2 | g4375 | g4375.t6 | exon | g4375.t6.exon1 | 1725324 | 1725654 |
| chr_2 | g4375 | g4375.t6 | cds | g4375.t6.CDS1 | 1725358 | 1725654 |
| chr_2 | g4375 | g4375.t6 | exon | g4375.t6.exon2 | 1725714 | 1726223 |
| chr_2 | g4375 | g4375.t6 | cds | g4375.t6.CDS2 | 1725714 | 1726223 |
| chr_2 | g4375 | g4375.t6 | TTS | g4375.t6 | 1726420 | 1726420 |
| chr_2 | g4375 | g4375.t6 | TSS | g4375.t6 | NA | NA |
Sequences
>g4375.t6 Gene=g4375 Length=841
TTTTGGAGGTAATGACGCAAATTGTGGAACATGGATGGATAAAATGGGATCTTCACAGAA
GGCTAATAACAAAGGTGTTCCATCTACTCCTCGTGACGGTTCTGCAGTTGAATTGGTCGG
ATTGCAAGCAAGTGTATTGAAATTTTTGTCATCATGCTCTGATTATCCATACAAATCTGT
AGAACGGAAGAATAAAGATAGTAATGAAACTATTTCTTGGTCTTTCAAAGAATGGGCAGA
AAAAATTGAAAAGAACTTTGAAAAATATTTCTATGTAGATGAAAACGATAGCAATACTCT
TGTTCATAAGCGAAAAATTTATAAAGACACACACGGAGCAAGTAGAAGATTTGCTGATTT
TCAATTAAGATGCAACTTTCCGATAGCAATGGTCGTTGCTCCTCAGCTGTTCAATCCGGA
TCATGCATGGGAAGCATTGGAAATGGCTCGTAAACACCTTCTTGGTCCACTTGGAATGAA
GACACTTGATCCTGATGATTGGTCTTATCGTGGAAATTATGATAACTCTAATGATAGTGA
TGACCCGAAAGTAGCACACGGAGCAAATTATCATCAAGGACCTGAATGGCTCTGGCCTAT
TGGTTACTATTTGCGTGCACGTTTGATTTTTGCTAAAAAATTGGGTAAATTGAAGGAAAC
ACAAGCAGAAACATGGAGCATTTTGACAGCACATTTGAAAGAATTGAGAACATCACCATG
GCGTGGATTACCTGAATTGACTAATGAAAATGGATCATTCTGTAGTGGATCGTGCACAAC
ACAAGCATGGTCTGTTGCTACAATTCTTGAAACTCTCTATGATTTGGAAAATCATAAATA
A
>g4375.t6 Gene=g4375 Length=268
MDKMGSSQKANNKGVPSTPRDGSAVELVGLQASVLKFLSSCSDYPYKSVERKNKDSNETI
SWSFKEWAEKIEKNFEKYFYVDENDSNTLVHKRKIYKDTHGASRRFADFQLRCNFPIAMV
VAPQLFNPDHAWEALEMARKHLLGPLGMKTLDPDDWSYRGNYDNSNDSDDPKVAHGANYH
QGPEWLWPIGYYLRARLIFAKKLGKLKETQAETWSILTAHLKELRTSPWRGLPELTNENG
SFCSGSCTTQAWSVATILETLYDLENHK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4375.t6 | Coils | Coil | Coil | 262 | 268 | - |
| 4 | g4375.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 18 | - |
| 5 | g4375.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 22 | - |
| 2 | g4375.t6 | PANTHER | PTHR10569 | GLYCOGEN DEBRANCHING ENZYME | 1 | 266 | 1.1E-114 |
| 1 | g4375.t6 | Pfam | PF06202 | Amylo-alpha-1,6-glucosidase | 1 | 259 | 3.9E-76 |
| 3 | g4375.t6 | SUPERFAMILY | SSF48208 | Six-hairpin glycosidases | 20 | 267 | 3.32E-31 |
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:0005975 | carbohydrate metabolic 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.
