Gene loci information

Transcript annotation

  • This transcript has been annotated as 1-4-alpha-glucan-branching enzyme.

Parent gene

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.t6 TSS g10493.t6 10195476 10195476
chr_1 g10493 g10493.t6 isoform g10493.t6 10195634 10199020
chr_1 g10493 g10493.t6 exon g10493.t6.exon1 10195634 10196272
chr_1 g10493 g10493.t6 exon g10493.t6.exon2 10196592 10197368
chr_1 g10493 g10493.t6 cds g10493.t6.CDS1 10196816 10197368
chr_1 g10493 g10493.t6 exon g10493.t6.exon3 10197430 10197928
chr_1 g10493 g10493.t6 cds g10493.t6.CDS2 10197430 10197928
chr_1 g10493 g10493.t6 exon g10493.t6.exon4 10198261 10198400
chr_1 g10493 g10493.t6 cds g10493.t6.CDS3 10198261 10198400
chr_1 g10493 g10493.t6 exon g10493.t6.exon5 10198562 10198646
chr_1 g10493 g10493.t6 cds g10493.t6.CDS4 10198562 10198646
chr_1 g10493 g10493.t6 exon g10493.t6.exon6 10198717 10199020
chr_1 g10493 g10493.t6 cds g10493.t6.CDS5 10198717 10199020
chr_1 g10493 g10493.t6 TTS g10493.t6 10199160 10199160

Sequences

>g10493.t6 Gene=g10493 Length=2444
ATGGATACGACAAAAATTGAAATAAAAAATATTCAAAAATTACTGAATCGGGATCATTAT
TTGAAGTCTTATGAGACTGAAATACGTAGAAGGTTTGTTTATGTTTACTATATGATTTTC
TAAAGAATTCCTTTGTGTTGATGCAAAATTTTAACTCATTTAATAGCAATTGAATTTTTT
CAAAGTCACGCCAAGGTCGATCATCTGTTTTTATATGAAAGCGAAAGAATATGAGAAATT
CTGAATTGGATAAAACGAAAAGTTTTTCTTGTTATTCTTTAATTTATTTCCACTTTGTTT
TCCTTCGCTGGATATTTACTCAACCATCAAAAAAATCCTTCCATGAAAATTGTTCTCATA
CCAGAGAAAAGTTTAATTTTACGTAATGTTCTTTTGATATTTTGCATCGTTTGTTTATTT
ACTTATTTGTGCTGACTTGTGACCTTTTTTCCTCACAATTTTCATTTAGACACGGATGCT
TGCAGCAGTGGCTCAAAACATTTGAAGATTCTGAAGGCGGTATAGAAACCTTCACAAAGG
GATATGAATTTTATGGGATACATGTAAAAGATGATAATTCACTCTTTGCGAGAGAATGGG
CACCTGGCGCTGTTGCCTTATATTTAACTGGAGAATTTAACAATTGGCATTGGGAAGCGA
CTCCTTATAAAAAATTAGAGTTTGGAAAGTGGGAATTAATCTTGCCTCCAAATGCTGATG
GCAGTTGTCAAATTGCTCATCTTAGTGAAATCAAAGTAATTGTTAGAACAAATGATGGTC
AACTTGTACCTAGACTATCACCATGGGCTAAATATGTTGTGCAGCCAACAGATTTAACAT
ACGGTTCAAACTACAAGCAGCTTATGTATCATCCACCTAAATCATCAATTTATCGATTTC
AACATAAGAAACCGGCAATAATCCCAAAATCATTAAGAATTTACGAGTGCCATGTGGGAA
TCGCAACAGAAAAACTTGAGGTTGGCTCTTATCGAAATTTTGCTGACAATGTAATTCCAC
GGATTGTGCGTCAGGGCTATAACACGATTCAAGTTATGGCCATTATGGAACATGCTTATT
ATGCTAGTTTTGGCTATCAAGTAACGAGTTTCTTTGCTGCATCATCACGTTATGGAACTC
CTGATGACCTAAAGTATCTCATCGATATTGCTCATAAAAACAATTTAATCGTCTTACTTG
ATGTGGTACATTCACACGCTAGCAAGAATGTTCTTGATGGACTGAATGAATTTGATGGAA
CCAATTCTTGTTATTTCCATGCACCACCACGTGGTGACCATGTATTATGGGATTCAAGAT
TGTTCAATTATGCATCATATGAAGTGCTTCGATTTTTACTCTCAAATTTAAGATGGTGGA
AAGACGAATATAATTTTGATGGTTATCGATTTGATGGAGTAACGTCAATGCTTTATCACA
ATCATGGTATTGGAACTGGTTTCTCTGGCGATTATAGTGAATATTTTGGACTAAATGTTG
ACACAGATGCTCTCATTTATTTAGCACTTGCTAATAAAATTCTGCATGACTTAGACCCAA
ATATCATCACAATTGCGGAGGATGTAAGTGGCATGCCAACTCTCTGCTGTCCAATTGACG
AAGGTGGTATTGGATTCGATTATCGCTTGGGTATGGCTATCCCTGATAAGTGGATTGAAA
TACTGAAAGAAAAGCGAGATGAAGATTGGAATATGGGCAATATTGTGCACACGTTGTCAA
ATCGACGATGGAAAGAGAAGACTGTTGCTTATGCTGAGTCACATGATCAAGCATTAGTTG
GCGACAAAACACTCGCTTTTTGGCTTATGGATAAAGAAATGTACACAAGCATGTCAGTTC
TTTCACCACCAAACCTCATTGTTGATCGTGGAATTGCTTTACACAAGATTATTAGGCTGA
TAACACACTCACTCGGTGGAGAAGCATATTTGAATTTCATGGGCAACGAATTCGGACATC
CGGAATGGCTTGACTTTCCGAGAGTTGGAAACAATCAGTCCTATCATTATTGTAGACGAC
AATGGAATCTTGTTGATGATTCAAATCTCAAATATAAATATCTCAATGATTTCGATAGGG
CGATGAATTTGACAGAGGAAAAATATGGTTGGCTTAATAGTAATCCAGGTTACGTGACAT
GGGCTCATGAGGGCGATAAGATTATCAGTTTCGAACGCAATGGTCATTTGTTTGTGTTCA
ACTTTCATATGGACCGAGCATTCACAGATTATCGTATTGGTGTAGAACGACCAGGAAGCT
ATAAAATTGTACTAAGCTCGGACGATGTAGCTTTTGGGGGATTTGGTCGTGTTGACTGTA
GTTTAACACACGTATCAGTACCGGAGGGTCATGCAGGTCGTAGTCAGTTTATTCACACAT
ATTTACCACCACGTACGGGCTTTGTTTTTGTGAGAGTTGGCTGA

>g10493.t6 Gene=g10493 Length=526
MYHPPKSSIYRFQHKKPAIIPKSLRIYECHVGIATEKLEVGSYRNFADNVIPRIVRQGYN
TIQVMAIMEHAYYASFGYQVTSFFAASSRYGTPDDLKYLIDIAHKNNLIVLLDVVHSHAS
KNVLDGLNEFDGTNSCYFHAPPRGDHVLWDSRLFNYASYEVLRFLLSNLRWWKDEYNFDG
YRFDGVTSMLYHNHGIGTGFSGDYSEYFGLNVDTDALIYLALANKILHDLDPNIITIAED
VSGMPTLCCPIDEGGIGFDYRLGMAIPDKWIEILKEKRDEDWNMGNIVHTLSNRRWKEKT
VAYAESHDQALVGDKTLAFWLMDKEMYTSMSVLSPPNLIVDRGIALHKIIRLITHSLGGE
AYLNFMGNEFGHPEWLDFPRVGNNQSYHYCRRQWNLVDDSNLKYKYLNDFDRAMNLTEEK
YGWLNSNPGYVTWAHEGDKIISFERNGHLFVFNFHMDRAFTDYRIGVERPGSYKIVLSSD
DVAFGGFGRVDCSLTHVSVPEGHAGRSQFIHTYLPPRTGFVFVRVG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g10493.t6 CDD cd11321 AmyAc_bac_euk_BE 4 412 0.0e+00
8 g10493.t6 Gene3D G3DSA:3.20.20.80 Glycosidases 4 425 0.0e+00
7 g10493.t6 Gene3D G3DSA:2.60.40.1180 - 426 526 0.0e+00
3 g10493.t6 PANTHER PTHR43651 1,4-ALPHA-GLUCAN-BRANCHING ENZYME 2 522 0.0e+00
9 g10493.t6 PIRSF PIRSF000463 GlgB 1 525 0.0e+00
2 g10493.t6 Pfam PF00128 Alpha amylase, catalytic domain 69 123 0.0e+00
1 g10493.t6 Pfam PF02806 Alpha amylase, C-terminal all-beta domain 431 523 0.0e+00
6 g10493.t6 SMART SM00642 aamy 46 411 4.1e-05
5 g10493.t6 SUPERFAMILY SSF51445 (Trans)glycosidases 18 418 0.0e+00
4 g10493.t6 SUPERFAMILY SSF51011 Glycosyl hydrolase domain 427 524 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: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.

Raw TPM values