Gene loci information

Transcript annotation

  • This transcript has been annotated as Alpha-amylase B.

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 g6053 g6053.t24 TSS g6053.t24 13890242 13890242
chr_2 g6053 g6053.t24 isoform g6053.t24 13890291 13892251
chr_2 g6053 g6053.t24 exon g6053.t24.exon1 13890291 13890343
chr_2 g6053 g6053.t24 cds g6053.t24.CDS1 13890291 13890343
chr_2 g6053 g6053.t24 exon g6053.t24.exon2 13890409 13890509
chr_2 g6053 g6053.t24 cds g6053.t24.CDS2 13890409 13890509
chr_2 g6053 g6053.t24 exon g6053.t24.exon3 13890563 13890632
chr_2 g6053 g6053.t24 cds g6053.t24.CDS3 13890563 13890632
chr_2 g6053 g6053.t24 exon g6053.t24.exon4 13890692 13890915
chr_2 g6053 g6053.t24 cds g6053.t24.CDS4 13890692 13890915
chr_2 g6053 g6053.t24 exon g6053.t24.exon5 13890977 13891138
chr_2 g6053 g6053.t24 cds g6053.t24.CDS5 13890977 13891138
chr_2 g6053 g6053.t24 exon g6053.t24.exon6 13891276 13891506
chr_2 g6053 g6053.t24 cds g6053.t24.CDS6 13891276 13891506
chr_2 g6053 g6053.t24 exon g6053.t24.exon7 13891629 13892251
chr_2 g6053 g6053.t24 cds g6053.t24.CDS7 13891629 13892251
chr_2 g6053 g6053.t24 TTS g6053.t24 13892345 13892345

Sequences

>g6053.t24 Gene=g6053 Length=1464
ATGAAACTTTTAGTTGTAATTTTGAGCATTTTTGTAGCTGTCAATGCTCAATGGGACACT
CATTGGTGGAGTGGTCGAAGTGGAATTGTTCATTTATTTGAGTGGAAATGGAATGATATT
GCAAATGAATGTGAAACATTCTTAGCACCAAATGGTTACGCGGGAGTCCAAACTTCACCT
CCGTCAGAAAATTTAGTCATCGGAAATCGACCCTGGTGGGAAAGATATCAGCCAGTTTCA
TATCATTTGAATACACGATCAGGTGATAGAAATGCATTCGCTGATATGGTTAGACGATGC
AATGCTGTTGGTATTCGTATCTATCCTGATGTTGTAATTAATCATATGGCGGCTGGTGAT
GGTTATGGAACAGGCGGAAGTGAATCTAGAGTTAGCCAATTAAGCTTCCCAGCTGTTCCA
TATGGAAGTAATGACTTCAATCCAAGATGTGATATCACTAATTACAATGATCCATATCAA
GTTAGAAACTGCTGGCTTGTTGGTTTATCTGATCTTAAGACAGGAAGTGATTATGTCCGT
CAGAAAATTGCCGATTTCTTAAATGATTTGATTAGTCTTGGTGTTGCAGGTAATTTCGTC
TTAATTTTAACAGATGTTCAGAATATTGTCTCACGCCTCAACAATTTGAACACAAACCAC
GGTTTCCCAGCCAACGCCCGTCCATTTATCACACAGGAAGTTATTGATTTGGGTGGTGAA
GCAATTAAAAAAGACGAATATTTGCACATTGGAACAATCACAGAGTTTAGATACAGTGCT
GAAATTGGACGAGTTTTCCGTGGTTATGATTTATTGAAATATCTTAAGAACTTTGGTGAA
GGATGGGGTTTTATGGCATCAGCATCAGCTCTTACTTTTGTTGACAATCACGACAACCAG
AGAGGACATGGAGCGGGAGGTGCCAATGTTCTCACATATAAAGTCTCAAAGAATTACAAA
ATGGCAACAGCTTTCCATCTCGCATGGAATTACGGAATTCCTCGTATCATGAGTAGCTTT
GCTTTCAATGATGGCGATCAAGGTCCACCAGCTGATGGCTATGGTAATTTGAAATCACCA
GAATTTAATTCAGAAGGAGCTTGCACTAATGGATGGGTTTGCGAACATCGTTGGAGACAA
ATTTACAACATGGTTAAATTCCGTAATGCAGCTGGTGGTGCAGCTGTACAAAATTGGTGG
GAAAATGGAAGCGGAAAACAGATTGCTTTCTCACGTGGCAACAGAGCTTTCATTGCCTTT
AATTTGGACTCATATGGCATCAATCAAAATTTGTACACAGGATTACCAGCTGGAACTTAT
TGTGAAATTGCATCAGGAAGCAAGAGCGGTTCAAGTTGCACAGGAAAAACAATTACAGTC
GATGGCAGTGGAAATGCCTACATTGATTTACCACACAATGCTGACGACGGTTTTGTTGCA
ATTCATGTTGATGCGAAATTGTAA

>g6053.t24 Gene=g6053 Length=487
MKLLVVILSIFVAVNAQWDTHWWSGRSGIVHLFEWKWNDIANECETFLAPNGYAGVQTSP
PSENLVIGNRPWWERYQPVSYHLNTRSGDRNAFADMVRRCNAVGIRIYPDVVINHMAAGD
GYGTGGSESRVSQLSFPAVPYGSNDFNPRCDITNYNDPYQVRNCWLVGLSDLKTGSDYVR
QKIADFLNDLISLGVAGNFVLILTDVQNIVSRLNNLNTNHGFPANARPFITQEVIDLGGE
AIKKDEYLHIGTITEFRYSAEIGRVFRGYDLLKYLKNFGEGWGFMASASALTFVDNHDNQ
RGHGAGGANVLTYKVSKNYKMATAFHLAWNYGIPRIMSSFAFNDGDQGPPADGYGNLKSP
EFNSEGACTNGWVCEHRWRQIYNMVKFRNAAGGAAVQNWWENGSGKQIAFSRGNRAFIAF
NLDSYGINQNLYTGLPAGTYCEIASGSKSGSSCTGKTITVDGSGNAYIDLPHNADDGFVA
IHVDAKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g6053.t24 CDD cd11317 AmyAc_bac_euk_AmyA 26 391 0.0
13 g6053.t24 Gene3D G3DSA:3.20.20.80 Glycosidases 18 393 1.3E-160
12 g6053.t24 Gene3D G3DSA:2.60.40.1180 - 394 487 2.0E-33
3 g6053.t24 PANTHER PTHR43447 ALPHA-AMYLASE 16 487 7.3E-158
4 g6053.t24 PANTHER PTHR43447:SF7 ALPHA-AMYLASE 16 487 7.3E-158
6 g6053.t24 PRINTS PR00110 Alpha-amylase signature 72 89 7.1E-26
5 g6053.t24 PRINTS PR00110 Alpha-amylase signature 104 115 7.1E-26
8 g6053.t24 PRINTS PR00110 Alpha-amylase signature 229 247 7.1E-26
7 g6053.t24 PRINTS PR00110 Alpha-amylase signature 288 300 7.1E-26
2 g6053.t24 Pfam PF00128 Alpha amylase, catalytic domain 82 330 3.9E-7
1 g6053.t24 Pfam PF02806 Alpha amylase, C-terminal all-beta domain 402 472 5.3E-13
15 g6053.t24 Phobius SIGNAL_PEPTIDE Signal peptide region 1 16 -
16 g6053.t24 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
17 g6053.t24 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 11 -
18 g6053.t24 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 12 16 -
14 g6053.t24 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 17 487 -
21 g6053.t24 SMART SM00642 aamy 27 388 1.5E-80
22 g6053.t24 SMART SM00632 Aamy_c 397 486 3.2E-43
10 g6053.t24 SUPERFAMILY SSF51445 (Trans)glycosidases 19 390 9.64E-89
9 g6053.t24 SUPERFAMILY SSF51011 Glycosyl hydrolase domain 396 486 9.16E-32
11 g6053.t24 SignalP_EUK SignalP-noTM SignalP-noTM 1 16 -
20 g6053.t24 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 18 -

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. There were no conditions that were differentially expressed