Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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 g6053 g6053.t7 TSS g6053.t7 13890242 13890242
chr_2 g6053 g6053.t7 isoform g6053.t7 13890291 13891489
chr_2 g6053 g6053.t7 exon g6053.t7.exon1 13890291 13890915
chr_2 g6053 g6053.t7 cds g6053.t7.CDS1 13890753 13890915
chr_2 g6053 g6053.t7 exon g6053.t7.exon2 13890977 13891204
chr_2 g6053 g6053.t7 cds g6053.t7.CDS2 13890977 13891194
chr_2 g6053 g6053.t7 exon g6053.t7.exon3 13891263 13891489
chr_2 g6053 g6053.t7 TTS g6053.t7 13892345 13892345

Sequences

>g6053.t7 Gene=g6053 Length=1080
ATGAAACTTTTAGTTGTAATTTTGAGCATTTTTGTAGCTGTCAATGCTCAATGGTGAGAA
AAAGTTTTAAAAATAAAAATCAAAGTTCAAGTACTAAGAAAATTATTTTAAAAATTAGGG
ACACTCATTGGTGGAGTGGTCGAAGTGGAATTGTTCATTTATTTGAGTGGAAATGGAATG
ATATTGCAAATGAATGTGAAACATTCTTAGCACCAAATGGTAACAAAATAAGAAAAATAT
TATGTGTAAAATTTAATAAATTAAAATTTTAGGTTACGCGGGAGTCCAAACTTCACCTCC
GTCAGAAAATTTAGTCATCGGAAATCGACCCTGGTGGGAAAGGTTAAAAATTTATTAAAA
TTCTTATCAAATGGAATTTGAAATTTGATTTTTTTCTTTAGATATCAGCCAGTTTCATAT
CATTTGAATACACGATCAGGTGATAGAAATGCATTCGCTGATATGGTTAGACGATGCAAT
GCTGTTGGTATTCGTATCTATCCTGATGTTGTAATTAATCATATGGCGGCTGGTGATGGT
TATGGAACAGGCGGAAGTGAATCTAGAGTTAGCCAATTAAGCTTCCCAGCTGTTCCATAT
GGAAGTAATGACTTCAATCCAAGATGTGATATCACTAATTACAATGATCCATATCAAGTT
AGAAACTGCTGGCTTGTTGGTTTATCTGATCTTAAGACAGGAAGTGATTATGTCCGTCAG
AAAATTGCCGATTTCTTAAATGATTTGATTAGTCTTGGTGTTGCAGGTAATTTCGTCTTA
ATTTTAAGTGTTTTCGACGAAATAAAAAATATTTCTTATCTCTTATCAAGGTTTTCGTAT
TGATGCCGTAAAGCACATGTGGCCAGCAGATGTTCAGAATATTGTCTCACGCCTCAACAA
TTTGAACACAAACCACGGTTTCCCAGCCAACGCCCGTCCATTTATCACACAGGAAGTTAT
TGATTTGGGTGGTGAAGCAATTAAAAAAGACGAATATTTGCACATTGGAACAATCACAGA
GTTTAGATACAGTGCTGAAATTGGACGAGTTTTCCGTGGTTATGATTTATTGAAATATCT

>g6053.t7 Gene=g6053 Length=126
MVRRCNAVGIRIYPDVVINHMAAGDGYGTGGSESRVSQLSFPAVPYGSNDFNPRCDITNY
NDPYQVRNCWLVGLSDLKTGSDYVRQKIADFLNDLISLGVAGNFVLILSVFDEIKNISYL
LSRFSY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g6053.t7 Gene3D G3DSA:3.20.20.80 Glycosidases 1 106 1.3E-42
1 g6053.t7 PANTHER PTHR43447 ALPHA-AMYLASE 1 102 9.1E-33
2 g6053.t7 PANTHER PTHR43447:SF7 ALPHA-AMYLASE 1 102 9.1E-33
5 g6053.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 90 -
7 g6053.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 91 111 -
6 g6053.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 112 126 -
3 g6053.t7 SUPERFAMILY SSF51445 (Trans)glycosidases 1 102 1.6E-26

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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