Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Maltase 1.

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_2 g5993 g5993.t2 TSS g5993.t2 13218283 13218283
chr_2 g5993 g5993.t2 isoform g5993.t2 13218299 13218944
chr_2 g5993 g5993.t2 exon g5993.t2.exon1 13218299 13218539
chr_2 g5993 g5993.t2 cds g5993.t2.CDS1 13218299 13218539
chr_2 g5993 g5993.t2 exon g5993.t2.exon2 13218599 13218756
chr_2 g5993 g5993.t2 cds g5993.t2.CDS2 13218599 13218756
chr_2 g5993 g5993.t2 exon g5993.t2.exon3 13218819 13218944
chr_2 g5993 g5993.t2 cds g5993.t2.CDS3 13218819 13218944
chr_2 g5993 g5993.t2 TTS g5993.t2 NA NA

Sequences

>g5993.t2 Gene=g5993 Length=525
ATGAAGTGGTTAGTATTAATAAATTTACTAATAGCAGTGATAACTGTAAAAGCAGGCTGG
CTGCCATTTTGGGTAGATGAAGAAGTAGAAGTTGAACTTTCTAACGAATTTGATTGGTGG
GAAAATGGAGTATTTTATCAAATTTATCCAAGATCATTTAAAGATGACAATAATGATGGA
ACTGGTGATATCAAGGGAATTATTTCGAAACTTGAACACTTGAAAGATTTGGGAGTAACA
GGAACTTGGCTTAGTCCAATTTTTAAAAGTCCTATGGTCGATGGAGGCTACGATATTTCA
GATTATACTGATGTCAATGAAATTTATGGAACTAAAGAAGATTTAAAAGCATTATTTGAT
AAAGCAAAAGAACTTGGACTTAAAATTATTCTTGACTTTGTGCCAAATCACTCAAGTGAT
CAACACGAGTGGTTCCAAAAATCAGTAAATAATGTTTCAGAATATGCAAATTATTATACA
TGGCGTGAATGTGAATTAGTTAATGCAACAACTGGTGAAAGAAGA

>g5993.t2 Gene=g5993 Length=175
MKWLVLINLLIAVITVKAGWLPFWVDEEVEVELSNEFDWWENGVFYQIYPRSFKDDNNDG
TGDIKGIISKLEHLKDLGVTGTWLSPIFKSPMVDGGYDISDYTDVNEIYGTKEDLKALFD
KAKELGLKIILDFVPNHSSDQHEWFQKSVNNVSEYANYYTWRECELVNATTGERR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g5993.t2 Gene3D G3DSA:3.20.20.80 Glycosidases 38 138 3.6E-68
8 g5993.t2 Gene3D G3DSA:3.90.400.10 - 139 167 3.6E-68
2 g5993.t2 PANTHER PTHR10357:SF207 LP11544P-RELATED 26 174 1.0E-65
3 g5993.t2 PANTHER PTHR10357 ALPHA-AMYLASE FAMILY MEMBER 26 174 1.0E-65
1 g5993.t2 Pfam PF00128 Alpha amylase, catalytic domain 62 164 5.2E-45
10 g5993.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 18 -
11 g5993.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
12 g5993.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 14 -
13 g5993.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 18 -
9 g5993.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 19 175 -
5 g5993.t2 SMART SM00642 aamy 47 175 6.5E-5
4 g5993.t2 SUPERFAMILY SSF51445 (Trans)glycosidases 33 166 7.28E-57
6 g5993.t2 SignalP_EUK SignalP-noTM SignalP-noTM 1 18 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5993/g5993.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5993.t2.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005975 carbohydrate metabolic process BP
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