General information for g10493.t1
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 g10493 is located on chr_1: 10197943..10199020 (+ 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 | g10493 | g10493.t1 | TSS | g10493.t1 | 10195476 | 10195476 |
| chr_1 | g10493 | g10493.t1 | isoform | g10493.t1 | 10195634 | 10199020 |
| chr_1 | g10493 | g10493.t1 | exon | g10493.t1.exon1 | 10195634 | 10195725 |
| chr_1 | g10493 | g10493.t1 | cds | g10493.t1.CDS1 | 10195634 | 10195725 |
| chr_1 | g10493 | g10493.t1 | exon | g10493.t1.exon2 | 10196103 | 10196272 |
| chr_1 | g10493 | g10493.t1 | cds | g10493.t1.CDS2 | 10196103 | 10196272 |
| chr_1 | g10493 | g10493.t1 | exon | g10493.t1.exon3 | 10196592 | 10197368 |
| chr_1 | g10493 | g10493.t1 | cds | g10493.t1.CDS3 | 10196592 | 10197368 |
| chr_1 | g10493 | g10493.t1 | exon | g10493.t1.exon4 | 10197430 | 10197928 |
| chr_1 | g10493 | g10493.t1 | cds | g10493.t1.CDS4 | 10197430 | 10197928 |
| chr_1 | g10493 | g10493.t1 | exon | g10493.t1.exon5 | 10198261 | 10198400 |
| chr_1 | g10493 | g10493.t1 | cds | g10493.t1.CDS5 | 10198261 | 10198400 |
| chr_1 | g10493 | g10493.t1 | exon | g10493.t1.exon6 | 10198562 | 10198646 |
| chr_1 | g10493 | g10493.t1 | cds | g10493.t1.CDS6 | 10198562 | 10198646 |
| chr_1 | g10493 | g10493.t1 | exon | g10493.t1.exon7 | 10198717 | 10199020 |
| chr_1 | g10493 | g10493.t1 | cds | g10493.t1.CDS7 | 10198717 | 10199020 |
| chr_1 | g10493 | g10493.t1 | TTS | g10493.t1 | 10199160 | 10199160 |
Sequences
>g10493.t1 Gene=g10493 Length=2067
ATGGATACGACAAAAATTGAAATAAAAAATATTCAAAAATTACTGAATCGGGATCATTAT
TTGAAGTCTTATGAGACTGAAATACGTAGAAGACACGGATGCTTGCAGCAGTGGCTCAAA
ACATTTGAAGATTCTGAAGGCGGTATAGAAACCTTCACAAAGGGATATGAATTTTATGGG
ATACATGTAAAAGATGATAATTCACTCTTTGCGAGAGAATGGGCACCTGGCGCTGTTGCC
TTATATTTAACTGGAGAATTTAACAATTGGCATTGGGAAGCGACTCCTTATAAAAAATTA
GAGTTTGGAAAGTGGGAATTAATCTTGCCTCCAAATGCTGATGGCAGTTGTCAAATTGCT
CATCTTAGTGAAATCAAAGTAATTGTTAGAACAAATGATGGTCAACTTGTACCTAGACTA
TCACCATGGGCTAAATATGTTGTGCAGCCAACAGATTTAACATACGGTTCAAACTACAAG
CAGCTTATGTATCATCCACCTAAATCATCAATTTATCGATTTCAACATAAGAAACCGGCA
ATAATCCCAAAATCATTAAGAATTTACGAGTGCCATGTGGGAATCGCAACAGAAAAACTT
GAGGTTGGCTCTTATCGAAATTTTGCTGACAATGTAATTCCACGGATTGTGCGTCAGGGC
TATAACACGATTCAAGTTATGGCCATTATGGAACATGCTTATTATGCTAGTTTTGGCTAT
CAAGTAACGAGTTTCTTTGCTGCATCATCACGTTATGGAACTCCTGATGACCTAAAGTAT
CTCATCGATATTGCTCATAAAAACAATTTAATCGTCTTACTTGATGTGGTACATTCACAC
GCTAGCAAGAATGTTCTTGATGGACTGAATGAATTTGATGGAACCAATTCTTGTTATTTC
CATGCACCACCACGTGGTGACCATGTATTATGGGATTCAAGATTGTTCAATTATGCATCA
TATGAAGTGCTTCGATTTTTACTCTCAAATTTAAGATGGTGGAAAGACGAATATAATTTT
GATGGTTATCGATTTGATGGAGTAACGTCAATGCTTTATCACAATCATGGTATTGGAACT
GGTTTCTCTGGCGATTATAGTGAATATTTTGGACTAAATGTTGACACAGATGCTCTCATT
TATTTAGCACTTGCTAATAAAATTCTGCATGACTTAGACCCAAATATCATCACAATTGCG
GAGGATGTAAGTGGCATGCCAACTCTCTGCTGTCCAATTGACGAAGGTGGTATTGGATTC
GATTATCGCTTGGGTATGGCTATCCCTGATAAGTGGATTGAAATACTGAAAGAAAAGCGA
GATGAAGATTGGAATATGGGCAATATTGTGCACACGTTGTCAAATCGACGATGGAAAGAG
AAGACTGTTGCTTATGCTGAGTCACATGATCAAGCATTAGTTGGCGACAAAACACTCGCT
TTTTGGCTTATGGATAAAGAAATGTACACAAGCATGTCAGTTCTTTCACCACCAAACCTC
ATTGTTGATCGTGGAATTGCTTTACACAAGATTATTAGGCTGATAACACACTCACTCGGT
GGAGAAGCATATTTGAATTTCATGGGCAACGAATTCGGACATCCGGAATGGCTTGACTTT
CCGAGAGTTGGAAACAATCAGTCCTATCATTATTGTAGACGACAATGGAATCTTGTTGAT
GATTCAAATCTCAAATATAAATATCTCAATGATTTCGATAGGGCGATGAATTTGACAGAG
GAAAAATATGGTTGGCTTAATAGTAATCCAGGTTACGTGACATGGGCTCATGAGGGCGAT
AAGATTATCAGTTTCGAACGCAATGGTCATTTGTTTGTGTTCAACTTTCATATGGACCGA
GCATTCACAGATTATCGTATTGGTGTAGAACGACCAGGAAGCTATAAAATTGTACTAAGC
TCGGACGATGTAGCTTTTGGGGGATTTGGTCGTGTTGACTGTAGTTTAACACACGTATCA
GTACCGGAGGGTCATGCAGGTCGTAGTCAGTTTATTCACACATATTTACCACCACGTACG
GGCTTTGTTTTTGTGAGAGTTGGCTGA
>g10493.t1 Gene=g10493 Length=688
MDTTKIEIKNIQKLLNRDHYLKSYETEIRRRHGCLQQWLKTFEDSEGGIETFTKGYEFYG
IHVKDDNSLFAREWAPGAVALYLTGEFNNWHWEATPYKKLEFGKWELILPPNADGSCQIA
HLSEIKVIVRTNDGQLVPRLSPWAKYVVQPTDLTYGSNYKQLMYHPPKSSIYRFQHKKPA
IIPKSLRIYECHVGIATEKLEVGSYRNFADNVIPRIVRQGYNTIQVMAIMEHAYYASFGY
QVTSFFAASSRYGTPDDLKYLIDIAHKNNLIVLLDVVHSHASKNVLDGLNEFDGTNSCYF
HAPPRGDHVLWDSRLFNYASYEVLRFLLSNLRWWKDEYNFDGYRFDGVTSMLYHNHGIGT
GFSGDYSEYFGLNVDTDALIYLALANKILHDLDPNIITIAEDVSGMPTLCCPIDEGGIGF
DYRLGMAIPDKWIEILKEKRDEDWNMGNIVHTLSNRRWKEKTVAYAESHDQALVGDKTLA
FWLMDKEMYTSMSVLSPPNLIVDRGIALHKIIRLITHSLGGEAYLNFMGNEFGHPEWLDF
PRVGNNQSYHYCRRQWNLVDDSNLKYKYLNDFDRAMNLTEEKYGWLNSNPGYVTWAHEGD
KIISFERNGHLFVFNFHMDRAFTDYRIGVERPGSYKIVLSSDDVAFGGFGRVDCSLTHVS
VPEGHAGRSQFIHTYLPPRTGFVFVRVG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g10493.t1 | CDD | cd02854 | E_set_GBE_euk_N | 66 | 152 | 0.0e+00 |
| 13 | g10493.t1 | CDD | cd11321 | AmyAc_bac_euk_BE | 166 | 574 | 0.0e+00 |
| 11 | g10493.t1 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 18 | 581 | 0.0e+00 |
| 9 | g10493.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 54 | 171 | 0.0e+00 |
| 10 | g10493.t1 | Gene3D | G3DSA:2.60.40.1180 | - | 588 | 688 | 0.0e+00 |
| 4 | g10493.t1 | PANTHER | PTHR43651 | 1,4-ALPHA-GLUCAN-BRANCHING ENZYME | 12 | 684 | 0.0e+00 |
| 12 | g10493.t1 | PIRSF | PIRSF000463 | GlgB | 2 | 687 | 0.0e+00 |
| 1 | g10493.t1 | Pfam | PF02922 | Carbohydrate-binding module 48 (Isoamylase N-terminal domain) | 59 | 144 | 0.0e+00 |
| 3 | g10493.t1 | Pfam | PF00128 | Alpha amylase, catalytic domain | 233 | 285 | 0.0e+00 |
| 2 | g10493.t1 | Pfam | PF02806 | Alpha amylase, C-terminal all-beta domain | 593 | 685 | 0.0e+00 |
| 8 | g10493.t1 | SMART | SM00642 | aamy | 208 | 573 | 4.1e-05 |
| 6 | g10493.t1 | SUPERFAMILY | SSF81296 | E set domains | 52 | 152 | 0.0e+00 |
| 7 | g10493.t1 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 180 | 580 | 0.0e+00 |
| 5 | g10493.t1 | SUPERFAMILY | SSF51011 | Glycosyl hydrolase domain | 589 | 686 | 0.0e+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:0043169 | cation binding | MF |
| GO:0005978 | glycogen biosynthetic process | BP |
| GO:0004553 | hydrolase activity, hydrolyzing O-glycosyl compounds | MF |
| GO:0005975 | carbohydrate metabolic process | BP |
| GO:0003844 | 1,4-alpha-glucan branching enzyme activity | MF |
| GO:0003824 | catalytic activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00700 (1,4-alpha-glucan branching enzyme)
Pathway
- This transcript belongs to the following pathways
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.
