Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Deoxyribose-phosphate aldolase.

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 g4950 g4950.t2 TTS g4950.t2 6145318 6145318
chr_2 g4950 g4950.t2 isoform g4950.t2 6145418 6146530
chr_2 g4950 g4950.t2 exon g4950.t2.exon1 6145418 6145746
chr_2 g4950 g4950.t2 cds g4950.t2.CDS1 6145725 6145746
chr_2 g4950 g4950.t2 exon g4950.t2.exon2 6145822 6146035
chr_2 g4950 g4950.t2 cds g4950.t2.CDS2 6145822 6146035
chr_2 g4950 g4950.t2 exon g4950.t2.exon3 6146091 6146444
chr_2 g4950 g4950.t2 cds g4950.t2.CDS3 6146091 6146444
chr_2 g4950 g4950.t2 exon g4950.t2.exon4 6146503 6146530
chr_2 g4950 g4950.t2 cds g4950.t2.CDS4 6146503 6146530
chr_2 g4950 g4950.t2 TSS g4950.t2 6146616 6146616

Sequences

>g4950.t2 Gene=g4950 Length=925
ATGCATGTAAACGAAACCATTCCATTTGAACAATCGTGGATTGAAAATGTCAATATTCAA
TTGCGAGGTTTAGAAGCGGCTGTAAAATTAATTGTTTCTCATTGTCATGTCACATCTGAT
GAGAACATTGTTGCATTTGCTTTGAAAGCATTGACTCTTACAGATTTAACGACATTAGCA
GGAGATGATTGTGAATCTAATGTTGAACGATTATGTGTTCGTGCTTGTTATCCATTTTTC
AATCATTCCGTTAAAAATGACTCAAATGAGTTCTATAAGAGTTTACATACAGCTGCTGTG
TGTGTTTATCCATCTAAAGTGAAGAATGCTTATGACACTTTAAAGAGATTGAATATGCTC
GATAAAGTTCAAATAGCTTCGGTTGCTACTGGTTTCCCAACTGGCTTATACCCGTTACAG
TCACGTCTTGATGAAATTAAATATGCAATCGAAAATGGTGCGACAGAAATTGACATTGTA
ATAGATCGTAGTCTGGTGTTAACTCATAACTGGACTAAACTTTATGGGGAAGTAGTTGAA
ATGCGAAAAGCTTGCGGAAATCGTGCTCACTTAAAGACAATATTGGGTATTGGAGAGTAC
TATGGAGAATGTTTATAAAGCTTCCATGATATGTATGATGGCTGGTGCTGATTTCATAAA
AACAAGCACTGGAAAAGAGGTTGTTAATGCAACCCTTCCAGTTGGTTTATGTATGATTAG
AGCAATTCAAGAATTTCATCGTTTAACAAAAAAGAATGTTGGTCTTAAACCAGCTGGTGG
TGTTCGCACTGTAAATGATGCTATAAAATGGATAATTTTAATCAAAGAAACTCTTGGTAT
GGAATATCTTCAGCCACATCTCTTTCGCTTTGGTGCTTCTGGTTTACTGGATGATATTGA
AAAAGTCGTTAAAAGTAAATGTTAA

>g4950.t2 Gene=g4950 Length=205
MHVNETIPFEQSWIENVNIQLRGLEAAVKLIVSHCHVTSDENIVAFALKALTLTDLTTLA
GDDCESNVERLCVRACYPFFNHSVKNDSNEFYKSLHTAAVCVYPSKVKNAYDTLKRLNML
DKVQIASVATGFPTGLYPLQSRLDEIKYAIENGATEIDIVIDRSLVLTHNWTKLYGEVVE
MRKACGNRAHLKTILGIGEYYGECL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g4950.t2 Gene3D G3DSA:3.20.20.70 Aldolase class I 39 203 0
2 g4950.t2 PANTHER PTHR10889 DEOXYRIBOSE-PHOSPHATE ALDOLASE 3 199 0
3 g4950.t2 PANTHER PTHR10889:SF3 DEOXYRIBOSE-PHOSPHATE ALDOLASE 3 199 0
1 g4950.t2 Pfam PF01791 DeoC/LacD family aldolase 51 202 0
4 g4950.t2 SUPERFAMILY SSF51569 Aldolase 44 199 0

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:0016829 lyase activity MF
GO:0004139 deoxyribose-phosphate aldolase activity MF
GO:0003824 catalytic activity MF
GO:0005737 cytoplasm CC
GO:0009264 deoxyribonucleotide catabolic process BP

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