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.t4 TTS g13964.t4 33643589 33643589
chr_1 g13964 g13964.t4 isoform g13964.t4 33643858 33645003
chr_1 g13964 g13964.t4 exon g13964.t4.exon1 33643858 33644039
chr_1 g13964 g13964.t4 cds g13964.t4.CDS1 33643858 33644039
chr_1 g13964 g13964.t4 exon g13964.t4.exon2 33644101 33644932
chr_1 g13964 g13964.t4 cds g13964.t4.CDS2 33644101 33644932
chr_1 g13964 g13964.t4 exon g13964.t4.exon3 33644998 33645003
chr_1 g13964 g13964.t4 cds g13964.t4.CDS3 33644998 33645000
chr_1 g13964 g13964.t4 TSS g13964.t4 NA NA

Sequences

>g13964.t4 Gene=g13964 Length=1020
TCTATGCTTTATCATTCGCACGGTATTGGTGAGGGATTTTCGGGTGATTACAACGAATAT
TTTGGACTTAACGTTGATACCGACGCATTCGTTTATTTGGCATTGGCGAATAAGTTCCTT
CACGATTTGGATCCAAATGTCATCACAATCGCTGAAGACGTGAGCGGAATGCCGAGTCTT
TGTCGTCCATTCCATGAGGGTGGCGGTGGATTTGATTATCGTCTTGCAATGGCTATACCA
GACAAGTGGATTAAAGTCCTAAAAGAGCAATCTGATGAAGACTGGGATATTGGAAATATT
GTGCATACACTTACAAATCGTCGTTGGAAAGAGAAGGCAGTTGCATATGCTGAAAGTCAC
GATCAAGCACTCGTAGGTGATAAGACAATAGCCTTTTGGCTTATGGACAAGGAAATGTAT
TGGCAAATGTCAACCTTGGGTGATTCTTCATTAATTATCGATAGAGGCATAGCTTTGCAT
AAATTAATTCGTTTAATAACTAATGCACTTGGTGGTGAAGCATACTTGAATTTTATGGGT
AATGAATTTGGTCATCCTGAATGGCTTGATTTTCCTAGAATTGGTAATGGCGAGTCATAT
CATTATTGTCGCCGTCAATGGAGTCTTGTTGATGATGAATTGTTAAAGTACAAATTTTTG
AATAATTGGGATCGTGCAATGAATTTTACTGAAGAGAAATATGGTTGGTTGAGTGCAAAT
GATTCAGGCTATGTTAGTTGGAAACATCAAGATGATAAAGTTGTTGCTTTCGAACGAGTC
GGCCTTGTTTTTGTCATTAATTTTCATTCAACTAAAAGTTTTACTGATTATAAAGTTGGC
GTTGAAGTTCCTGGCAGTTATAAAATTGTATTGAATTCGGATGCTCCTGAATTTGGTGGA
TTTAATCGCATTGATTCGTCAAATGTTCATCAAACTTTTCCAGAGGGTTACGCTGGACGA
CGTAATCATATGTGCGTGTATATTCCAAGTCGCACAGCAATTGTTCTTGCTAAAGTCTGA

>g13964.t4 Gene=g13964 Length=338
MLYHSHGIGEGFSGDYNEYFGLNVDTDAFVYLALANKFLHDLDPNVITIAEDVSGMPSLC
RPFHEGGGGFDYRLAMAIPDKWIKVLKEQSDEDWDIGNIVHTLTNRRWKEKAVAYAESHD
QALVGDKTIAFWLMDKEMYWQMSTLGDSSLIIDRGIALHKLIRLITNALGGEAYLNFMGN
EFGHPEWLDFPRIGNGESYHYCRRQWSLVDDELLKYKFLNNWDRAMNFTEEKYGWLSAND
SGYVSWKHQDDKVVAFERVGLVFVINFHSTKSFTDYKVGVEVPGSYKIVLNSDAPEFGGF
NRIDSSNVHQTFPEGYAGRRNHMCVYIPSRTAIVLAKV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g13964.t4 Gene3D G3DSA:3.20.20.80 Glycosidases 1 237 0
6 g13964.t4 Gene3D G3DSA:2.60.40.1180 - 239 338 0
2 g13964.t4 PANTHER PTHR43651:SF2 1,4-ALPHA-GLUCAN-BRANCHING ENZYME, CHLOROPLASTIC/AMYLOPLASTIC 1 338 0
3 g13964.t4 PANTHER PTHR43651 1,4-ALPHA-GLUCAN-BRANCHING ENZYME 1 338 0
1 g13964.t4 Pfam PF02806 Alpha amylase, C-terminal all-beta domain 243 337 0
5 g13964.t4 SUPERFAMILY SSF51445 (Trans)glycosidases 7 208 0
4 g13964.t4 SUPERFAMILY SSF51011 Glycosyl hydrolase domain 242 336 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

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