Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t5 TSS g10493.t5 10195476 10195476
chr_1 g10493 g10493.t5 isoform g10493.t5 10195634 10196996
chr_1 g10493 g10493.t5 exon g10493.t5.exon1 10195634 10195725
chr_1 g10493 g10493.t5 exon g10493.t5.exon2 10195800 10196015
chr_1 g10493 g10493.t5 cds g10493.t5.CDS1 10195864 10196015
chr_1 g10493 g10493.t5 exon g10493.t5.exon3 10196103 10196272
chr_1 g10493 g10493.t5 cds g10493.t5.CDS2 10196103 10196272
chr_1 g10493 g10493.t5 exon g10493.t5.exon4 10196592 10196996
chr_1 g10493 g10493.t5 cds g10493.t5.CDS3 10196592 10196995
chr_1 g10493 g10493.t5 TTS g10493.t5 NA NA

Sequences

>g10493.t5 Gene=g10493 Length=883
ATGGATACGACAAAAATTGAAATAAAAAATATTCAAAAATTACTGAATCGGGATCATTAT
TTGAAGTCTTATGAGACTGAAATACGTAGAAGCAATTGAATTTTTTCAAAGTCACGCCAA
GGTCGATCATCTGTTTTTATATGAAAGCGAAAGAATATGAGAAATTCTGAATTGGATAAA
ACGAAAAGTTTTTCTTGTTATTCTTTAATTTATTTCCACTTTGTTTTCCTTCGCTGGATA
TTTACTCAACCATCAAAAAAATCCTTCCATGAAAATTGTTCTCATACCAGAGAAAAGTTT
AATTTTACACACGGATGCTTGCAGCAGTGGCTCAAAACATTTGAAGATTCTGAAGGCGGT
ATAGAAACCTTCACAAAGGGATATGAATTTTATGGGATACATGTAAAAGATGATAATTCA
CTCTTTGCGAGAGAATGGGCACCTGGCGCTGTTGCCTTATATTTAACTGGAGAATTTAAC
AATTGGCATTGGGAAGCGACTCCTTATAAAAAATTAGAGTTTGGAAAGTGGGAATTAATC
TTGCCTCCAAATGCTGATGGCAGTTGTCAAATTGCTCATCTTAGTGAAATCAAAGTAATT
GTTAGAACAAATGATGGTCAACTTGTACCTAGACTATCACCATGGGCTAAATATGTTGTG
CAGCCAACAGATTTAACATACGGTTCAAACTACAAGCAGCTTATGTATCATCCACCTAAA
TCATCAATTTATCGATTTCAACATAAGAAACCGGCAATAATCCCAAAATCATTAAGAATT
TACGAGTGCCATGTGGGAATCGCAACAGAAAAACTTGAGGTTGGCTCTTATCGAAATTTT
GCTGACAATGTAATTCCACGGATTGTGCGTCAGGGCTATAACA

>g10493.t5 Gene=g10493 Length=242
MRNSELDKTKSFSCYSLIYFHFVFLRWIFTQPSKKSFHENCSHTREKFNFTHGCLQQWLK
TFEDSEGGIETFTKGYEFYGIHVKDDNSLFAREWAPGAVALYLTGEFNNWHWEATPYKKL
EFGKWELILPPNADGSCQIAHLSEIKVIVRTNDGQLVPRLSPWAKYVVQPTDLTYGSNYK
QLMYHPPKSSIYRFQHKKPAIIPKSLRIYECHVGIATEKLEVGSYRNFADNVIPRIVRQG
YN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g10493.t5 CDD cd02854 E_set_GBE_euk_N 86 172 3.15401E-41
7 g10493.t5 Gene3D G3DSA:3.20.20.80 Glycosidases 46 242 2.9E-54
6 g10493.t5 Gene3D G3DSA:2.60.40.10 Immunoglobulins 74 191 2.9E-54
2 g10493.t5 PANTHER PTHR43651:SF3 1,4-ALPHA-GLUCAN-BRANCHING ENZYME 42 242 7.4E-54
3 g10493.t5 PANTHER PTHR43651 1,4-ALPHA-GLUCAN-BRANCHING ENZYME 42 242 7.4E-54
1 g10493.t5 Pfam PF02922 Carbohydrate-binding module 48 (Isoamylase N-terminal domain) 79 164 8.6E-12
8 g10493.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
10 g10493.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 29 -
9 g10493.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 30 242 -
5 g10493.t5 SUPERFAMILY SSF81296 E set domains 72 172 3.2E-15
4 g10493.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 12 29 -

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: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

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