General information for g13964.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 1-4-alpha-glucan-branching enzyme.
Parent gene
- The parent gene g13964 is located on chr_1: 33645150..33648109 (- 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_1 | g13964 | g13964.t3 | TTS | g13964.t3 | 33643589 | 33643589 |
| chr_1 | g13964 | g13964.t3 | isoform | g13964.t3 | 33643858 | 33644932 |
| chr_1 | g13964 | g13964.t3 | exon | g13964.t3.exon1 | 33643858 | 33644039 |
| chr_1 | g13964 | g13964.t3 | cds | g13964.t3.CDS1 | 33644004 | 33644039 |
| chr_1 | g13964 | g13964.t3 | exon | g13964.t3.exon2 | 33644105 | 33644932 |
| chr_1 | g13964 | g13964.t3 | cds | g13964.t3.CDS2 | 33644105 | 33644770 |
| chr_1 | g13964 | g13964.t3 | TSS | g13964.t3 | NA | NA |
Sequences
>g13964.t3 Gene=g13964 Length=1010
CTTTATCATTCGCACGGTATTGGTGAGGGATTTTCGGGTGATTACAACGAATATTTTGGA
CTTAACGTTGATACCGACGCATTCGTTTATTTGGCATTGGCGAATAAGTTCCTTCACGAT
TTGGATCCAAATGTCATCACAATCGCTGAAGACGTGAGCGGAATGCCGAGTCTTTGTCGT
CCATTCCATGAGGGTGGCGGTGGATTTGATTATCGTCTTGCAATGGCTATACCAGACAAG
TGGATTAAAGTCCTAAAAGAGCAATCTGATGAAGACTGGGATATTGGAAATATTGTGCAT
ACACTTACAAATCGTCGTTGGAAAGAGAAGGCAGTTGCATATGCTGAAAGTCACGATCAA
GCACTCGTAGGTGATAAGACAATAGCCTTTTGGCTTATGGACAAGGAAATGTATTGGCAA
ATGTCAACCTTGGGTGATTCTTCATTAATTATCGATAGAGGCATAGCTTTGCATAAATTA
ATTCGTTTAATAACTAATGCACTTGGTGGTGAAGCATACTTGAATTTTATGGGTAATGAA
TTTGGTCATCCTGAATGGCTTGATTTTCCTAGAATTGGTAATGGCGAGTCATATCATTAT
TGTCGCCGTCAATGGAGTCTTGTTGATGATGAATTGTTAAAGTACAAATTTTTGAATAAT
TGGGATCGTGCAATGAATTTTACTGAAGAGAAATATGGTTGGTTGAGTGCAAATGATTCA
GGCTATGTTAGTTGGAAACATCAAGATGATAAAGTTGTTGCTTTCGAACGAGTCGGCCTT
GTTTTTGTCATTAATTTTCATTCAACTAAAAGTTTTACTGATTATAAAGCGTTGAAGTTC
CTGGCAGTTATAAAATTGTATTGAATTCGGATGCTCCTGAATTTGGTGGATTTAATCGCA
TTGATTCGTCAAATGTTCATCAAACTTTTCCAGAGGGTTACGCTGGACGACGTAATCATA
TGTGCGTGTATATTCCAAGTCGCACAGCAATTGTTCTTGCTAAAGTCTGA
>g13964.t3 Gene=g13964 Length=233
MPSLCRPFHEGGGGFDYRLAMAIPDKWIKVLKEQSDEDWDIGNIVHTLTNRRWKEKAVAY
AESHDQALVGDKTIAFWLMDKEMYWQMSTLGDSSLIIDRGIALHKLIRLITNALGGEAYL
NFMGNEFGHPEWLDFPRIGNGESYHYCRRQWSLVDDELLKYKFLNNWDRAMNFTEEKYGW
LSANDSGYVSWKHQDDKVVAFERVGLVFVINFHSTKSFTDYKALKFLAVIKLY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g13964.t3 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 1 | 182 | 0.00e+00 |
| 6 | g13964.t3 | Gene3D | G3DSA:2.60.40.1180 | - | 184 | 225 | 0.00e+00 |
| 2 | g13964.t3 | PANTHER | PTHR43651:SF2 | 1,4-ALPHA-GLUCAN-BRANCHING ENZYME, CHLOROPLASTIC/AMYLOPLASTIC | 1 | 222 | 0.00e+00 |
| 3 | g13964.t3 | PANTHER | PTHR43651 | 1,4-ALPHA-GLUCAN-BRANCHING ENZYME | 1 | 222 | 0.00e+00 |
| 1 | g13964.t3 | Pfam | PF02806 | Alpha amylase, C-terminal all-beta domain | 188 | 223 | 7.00e-07 |
| 5 | g13964.t3 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 4 | 153 | 0.00e+00 |
| 4 | g13964.t3 | SUPERFAMILY | SSF51011 | Glycosyl hydrolase domain | 187 | 222 | 6.26e-05 |
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:0043169 | cation binding | MF |
| GO:0005978 | glycogen biosynthetic process | BP |
| GO:0005975 | carbohydrate metabolic process | BP |
| GO:0003844 | 1,4-alpha-glucan branching enzyme activity | MF |
| GO:0003824 | catalytic 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. There were no conditions that were differentially expressed