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 g13964 g13964.t2 TTS g13964.t2 33643589 33643589
chr_1 g13964 g13964.t2 isoform g13964.t2 33643858 33644932
chr_1 g13964 g13964.t2 exon g13964.t2.exon1 33643858 33644039
chr_1 g13964 g13964.t2 cds g13964.t2.CDS1 33643858 33644039
chr_1 g13964 g13964.t2 exon g13964.t2.exon2 33644101 33644932
chr_1 g13964 g13964.t2 cds g13964.t2.CDS2 33644101 33644770
chr_1 g13964 g13964.t2 TSS g13964.t2 NA NA

Sequences

>g13964.t2 Gene=g13964 Length=1014
CTTTATCATTCGCACGGTATTGGTGAGGGATTTTCGGGTGATTACAACGAATATTTTGGA
CTTAACGTTGATACCGACGCATTCGTTTATTTGGCATTGGCGAATAAGTTCCTTCACGAT
TTGGATCCAAATGTCATCACAATCGCTGAAGACGTGAGCGGAATGCCGAGTCTTTGTCGT
CCATTCCATGAGGGTGGCGGTGGATTTGATTATCGTCTTGCAATGGCTATACCAGACAAG
TGGATTAAAGTCCTAAAAGAGCAATCTGATGAAGACTGGGATATTGGAAATATTGTGCAT
ACACTTACAAATCGTCGTTGGAAAGAGAAGGCAGTTGCATATGCTGAAAGTCACGATCAA
GCACTCGTAGGTGATAAGACAATAGCCTTTTGGCTTATGGACAAGGAAATGTATTGGCAA
ATGTCAACCTTGGGTGATTCTTCATTAATTATCGATAGAGGCATAGCTTTGCATAAATTA
ATTCGTTTAATAACTAATGCACTTGGTGGTGAAGCATACTTGAATTTTATGGGTAATGAA
TTTGGTCATCCTGAATGGCTTGATTTTCCTAGAATTGGTAATGGCGAGTCATATCATTAT
TGTCGCCGTCAATGGAGTCTTGTTGATGATGAATTGTTAAAGTACAAATTTTTGAATAAT
TGGGATCGTGCAATGAATTTTACTGAAGAGAAATATGGTTGGTTGAGTGCAAATGATTCA
GGCTATGTTAGTTGGAAACATCAAGATGATAAAGTTGTTGCTTTCGAACGAGTCGGCCTT
GTTTTTGTCATTAATTTTCATTCAACTAAAAGTTTTACTGATTATAAAGTTGGCGTTGAA
GTTCCTGGCAGTTATAAAATTGTATTGAATTCGGATGCTCCTGAATTTGGTGGATTTAAT
CGCATTGATTCGTCAAATGTTCATCAAACTTTTCCAGAGGGTTACGCTGGACGACGTAAT
CATATGTGCGTGTATATTCCAAGTCGCACAGCAATTGTTCTTGCTAAAGTCTGA

>g13964.t2 Gene=g13964 Length=283
MPSLCRPFHEGGGGFDYRLAMAIPDKWIKVLKEQSDEDWDIGNIVHTLTNRRWKEKAVAY
AESHDQALVGDKTIAFWLMDKEMYWQMSTLGDSSLIIDRGIALHKLIRLITNALGGEAYL
NFMGNEFGHPEWLDFPRIGNGESYHYCRRQWSLVDDELLKYKFLNNWDRAMNFTEEKYGW
LSANDSGYVSWKHQDDKVVAFERVGLVFVINFHSTKSFTDYKVGVEVPGSYKIVLNSDAP
EFGGFNRIDSSNVHQTFPEGYAGRRNHMCVYIPSRTAIVLAKV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g13964.t2 Gene3D G3DSA:3.20.20.80 Glycosidases 1 182 0
6 g13964.t2 Gene3D G3DSA:2.60.40.1180 - 184 283 0
2 g13964.t2 PANTHER PTHR43651:SF2 1,4-ALPHA-GLUCAN-BRANCHING ENZYME, CHLOROPLASTIC/AMYLOPLASTIC 1 283 0
3 g13964.t2 PANTHER PTHR43651 1,4-ALPHA-GLUCAN-BRANCHING ENZYME 1 283 0
1 g13964.t2 Pfam PF02806 Alpha amylase, C-terminal all-beta domain 188 282 0
5 g13964.t2 SUPERFAMILY SSF51445 (Trans)glycosidases 4 153 0
4 g13964.t2 SUPERFAMILY SSF51011 Glycosyl hydrolase domain 187 281 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: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

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. There were no conditions that were differentially expressed