Gene loci information

Transcript annotation

  • This transcript has been annotated as Alpha-amylase-related protein.

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 g4715 g4715.t4 TTS g4715.t4 4358730 4358730
chr_2 g4715 g4715.t4 isoform g4715.t4 4359278 4361336
chr_2 g4715 g4715.t4 exon g4715.t4.exon1 4359278 4359794
chr_2 g4715 g4715.t4 cds g4715.t4.CDS1 4359782 4359794
chr_2 g4715 g4715.t4 exon g4715.t4.exon2 4360277 4360567
chr_2 g4715 g4715.t4 cds g4715.t4.CDS2 4360277 4360567
chr_2 g4715 g4715.t4 exon g4715.t4.exon3 4360966 4361336
chr_2 g4715 g4715.t4 cds g4715.t4.CDS3 4360966 4361336
chr_2 g4715 g4715.t4 TSS g4715.t4 4361363 4361363

Sequences

>g4715.t4 Gene=g4715 Length=1179
ATGCTTCGATCATTGCAATTGCTTCTCGGTGCAATTTGTTGTAGTGAATTTTTTATTCCT
CGTCCACAAGTTGCAGATTTACCAAAAGAAGTGAAGAGAAATTTTACTGATCCTCATTTT
TTAAGTGGTCATAATGGAATTGTGCAATTATTTGAATGGAAATGGTTAGATATAGCAAAA
GAATGTGAAGAATTTCTCGGTCCAAGGAAATTTGGTGGAGTTCAAATTTCTCCACCTAAT
GAAAATATTATTATTGAAAATAGACCGTGGTTCGAAAGATATCAACCAATTTCTTATAAA
ATTGCATCAAGATCTGGAAGTGAAAAAGAATTTTTAGAAATGACAAGACGATGCAATGCT
GTTGGTGTTAGAATTTATGCAGATATTGTCATAAATCATATGGCAGCTGATCAAGTAAAG
TACATAGCAAACGGCACAGGTGGATCACAAGCAATTCCTGCAGTTCGAAATTATCCAGCT
GTTCCTTATAGTATTTTTAATTTTCATCCAACTTGTGCAATTGTCAATTATCAGGATCCG
TATCAAGTCAGAAATTGTGAACTCGTTGGATTGCATGATCTTAATCAGACAATAGAAAAT
ACTAGAGATAGAATTGTTGAATATTTGAATCATTTGATTGATCTGGGAGTTGCTGGATTT
CGTTTTATTTCTTAGCTAAACACATGTGGCCAAAAGATCTTGAAATCATCACAAATCGAG
TCAAAAATTTAAATACAATCTTTGGTTTTGGACCAAATCTTGATCCATTTGTATATCAAG
AAGTGATTGATAATGGCAATGAGCCAATTAGTAAATATGAGTACACTTATGCTTGTGTCA
CAGAATTTCGTTTCTCATCTGAAATTGGCAAAGCATTTACAGGCGGTGATGAGCTTAGAT
GGCTGATTGGCTTTGGTGAAAAATGGGATTTATTGCCATCACATTTGGCAGTGACTTTTA
TTGATAATCATGATTCACAAAGAAGTGGTAGCAATGATATTTTAACATACAAAAGAAGGA
AAAATTATATAATGGCTCAAGCATTTTCTTTAGCACATCCTTATGGCATTAAAAGAATTA
TGAGTTCATTTTCATTCAATGACAATAATCAAGGACCACCAGCAGATGCCAATGGAACTA
TAATTTCACCAACAATAGATAAAAATGGAAATTGTACTA

>g4715.t4 Gene=g4715 Length=224
MLRSLQLLLGAICCSEFFIPRPQVADLPKEVKRNFTDPHFLSGHNGIVQLFEWKWLDIAK
ECEEFLGPRKFGGVQISPPNENIIIENRPWFERYQPISYKIASRSGSEKEFLEMTRRCNA
VGVRIYADIVINHMAADQVKYIANGTGGSQAIPAVRNYPAVPYSIFNFHPTCAIVNYQDP
YQVRNCELVGLHDLNQTIENTRDRIVEYLNHLIDLGVAGFRFIS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g4715.t4 Coils Coil Coil 191 211 -
9 g4715.t4 Gene3D G3DSA:3.20.20.80 Glycosidases 35 222 1.1E-78
2 g4715.t4 PANTHER PTHR43447 ALPHA-AMYLASE 37 222 1.0E-66
3 g4715.t4 PANTHER PTHR43447:SF5 PANCREATIC ALPHA-AMYLASE 37 222 1.0E-66
5 g4715.t4 PRINTS PR00110 Alpha-amylase signature 90 107 5.0E-11
4 g4715.t4 PRINTS PR00110 Alpha-amylase signature 122 133 5.0E-11
6 g4715.t4 PRINTS PR00110 Alpha-amylase signature 217 224 5.0E-11
1 g4715.t4 Pfam PF00128 Alpha amylase, catalytic domain 99 221 3.8E-7
12 g4715.t4 Phobius SIGNAL_PEPTIDE Signal peptide region 1 25 -
13 g4715.t4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
14 g4715.t4 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 14 -
15 g4715.t4 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 25 -
11 g4715.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 26 224 -
16 g4715.t4 SMART SM00642 aamy 45 224 7.2E-5
7 g4715.t4 SUPERFAMILY SSF51445 (Trans)glycosidases 41 222 1.57E-50
8 g4715.t4 SignalP_EUK SignalP-noTM SignalP-noTM 1 16 -

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:0004556 alpha-amylase activity MF
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.

Raw TPM values