General information for g4375.t5
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.t5 | isoform | g4375.t5 | 1725087 | 1726223 |
| chr_2 | g4375 | g4375.t5 | exon | g4375.t5.exon1 | 1725087 | 1725270 |
| chr_2 | g4375 | g4375.t5 | cds | g4375.t5.CDS1 | 1725138 | 1725270 |
| chr_2 | g4375 | g4375.t5 | exon | g4375.t5.exon2 | 1725323 | 1725654 |
| chr_2 | g4375 | g4375.t5 | cds | g4375.t5.CDS2 | 1725323 | 1725654 |
| chr_2 | g4375 | g4375.t5 | exon | g4375.t5.exon3 | 1725714 | 1726223 |
| chr_2 | g4375 | g4375.t5 | cds | g4375.t5.CDS3 | 1725714 | 1726223 |
| chr_2 | g4375 | g4375.t5 | TTS | g4375.t5 | 1726420 | 1726420 |
| chr_2 | g4375 | g4375.t5 | TSS | g4375.t5 | NA | NA |
Sequences
>g4375.t5 Gene=g4375 Length=1026
GACAGTGAAGCTAAACCAGCTGGAGAGTGTGATCAACTATTGTATGAAGTCATGCAAGAA
GCATTAAATGTTCACTTCCAAGGCCTTGTCTATCGTGAAAGAAATGCAGGAAAGCGAATC
GATGAACATATGACAGATCATGGTTTCAACAATCAAATTGGTATTCATCCAGAAACTGGA
TTTGTTTTTGGAGGTAATGACGCAAATTGTGGAACATGGATGGATAAAATGGGATCTTCA
CAGAAGGCTAATAACAAAGGTGTTCCATCTACTCCTCGTGACGGTTCTGCAGTTGAATTG
GTCGGATTGCAAGCAAGTGTATTGAAATTTTTGTCATCATGCTCTGATTATCCATACAAA
TCTGTAGAACGGAAGAATAAAGATAGTAATGAAACTATTTCTTGGTCTTTCAAAGAATGG
GCAGAAAAAATTGAAAAGAACTTTGAAAAATATTTCTATGTAGATGAAAACGATAGCAAT
ACTCTTGTTCATAAGCGAAAAATTTATAAAGACACACACGGAGCAAGTAGAAGATTTGCT
GATTTTCAATTAAGATGCAACTTTCCGATAGCAATGGTCGTTGCTCCTCAGCTGTTCAAT
CCGGATCATGCATGGGAAGCATTGGAAATGGCTCGTAAACACCTTCTTGGTCCACTTGGA
ATGAAGACACTTGATCCTGATGATTGGTCTTATCGTGGAAATTATGATAACTCTAATGAT
AGTGATGACCCGAAAGTAGCACACGGAGCAAATTATCATCAAGGACCTGAATGGCTCTGG
CCTATTGGTTACTATTTGCGTGCACGTTTGATTTTTGCTAAAAAATTGGGTAAATTGAAG
GAAACACAAGCAGAAACATGGAGCATTTTGACAGCACATTTGAAAGAATTGAGAACATCA
CCATGGCGTGGATTACCTGAATTGACTAATGAAAATGGATCATTCTGTAGTGGATCGTGC
ACAACACAAGCATGGTCTGTTGCTACAATTCTTGAAACTCTCTATGATTTGGAAAATCAT
AAATAA
>g4375.t5 Gene=g4375 Length=324
MQEALNVHFQGLVYRERNAGKRIDEHMTDHGFNNQIGIHPETGFVFGGNDANCGTWMDKM
GSSQKANNKGVPSTPRDGSAVELVGLQASVLKFLSSCSDYPYKSVERKNKDSNETISWSF
KEWAEKIEKNFEKYFYVDENDSNTLVHKRKIYKDTHGASRRFADFQLRCNFPIAMVVAPQ
LFNPDHAWEALEMARKHLLGPLGMKTLDPDDWSYRGNYDNSNDSDDPKVAHGANYHQGPE
WLWPIGYYLRARLIFAKKLGKLKETQAETWSILTAHLKELRTSPWRGLPELTNENGSFCS
GSCTTQAWSVATILETLYDLENHK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g4375.t5 | PANTHER | PTHR10569 | GLYCOGEN DEBRANCHING ENZYME | 1 | 322 | 0 |
| 1 | g4375.t5 | Pfam | PF06202 | Amylo-alpha-1,6-glucosidase | 1 | 315 | 0 |
| 3 | g4375.t5 | SUPERFAMILY | SSF48208 | Six-hairpin glycosidases | 49 | 323 | 0 |
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.
