General information for g4950.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Deoxyribose-phosphate aldolase.
Parent gene
- The parent gene g4950 is located on chr_2: 6146091..6146530 (- strand)
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.t1 | TTS | g4950.t1 | 6145318 | 6145318 |
| chr_2 | g4950 | g4950.t1 | isoform | g4950.t1 | 6145418 | 6146530 |
| chr_2 | g4950 | g4950.t1 | exon | g4950.t1.exon1 | 6145418 | 6145746 |
| chr_2 | g4950 | g4950.t1 | cds | g4950.t1.CDS1 | 6145418 | 6145746 |
| chr_2 | g4950 | g4950.t1 | exon | g4950.t1.exon2 | 6145817 | 6146035 |
| chr_2 | g4950 | g4950.t1 | cds | g4950.t1.CDS2 | 6145817 | 6146035 |
| chr_2 | g4950 | g4950.t1 | exon | g4950.t1.exon3 | 6146091 | 6146444 |
| chr_2 | g4950 | g4950.t1 | cds | g4950.t1.CDS3 | 6146091 | 6146444 |
| chr_2 | g4950 | g4950.t1 | exon | g4950.t1.exon4 | 6146503 | 6146530 |
| chr_2 | g4950 | g4950.t1 | cds | g4950.t1.CDS4 | 6146503 | 6146530 |
| chr_2 | g4950 | g4950.t1 | TSS | g4950.t1 | 6146616 | 6146616 |
Sequences
>g4950.t1 Gene=g4950 Length=930
ATGCATGTAAACGAAACCATTCCATTTGAACAATCGTGGATTGAAAATGTCAATATTCAA
TTGCGAGGTTTAGAAGCGGCTGTAAAATTAATTGTTTCTCATTGTCATGTCACATCTGAT
GAGAACATTGTTGCATTTGCTTTGAAAGCATTGACTCTTACAGATTTAACGACATTAGCA
GGAGATGATTGTGAATCTAATGTTGAACGATTATGTGTTCGTGCTTGTTATCCATTTTTC
AATCATTCCGTTAAAAATGACTCAAATGAGTTCTATAAGAGTTTACATACAGCTGCTGTG
TGTGTTTATCCATCTAAAGTGAAGAATGCTTATGACACTTTAAAGAGATTGAATATGCTC
GATAAAGTTCAAATAGCTTCGGTTGCTACTGGTTTCCCAACTGGCTTATACCCGTTACAG
TCACGTCTTGATGAAATTAAATATGCAATCGAAAATGGTGCGACAGAAATTGACATTGTA
ATAGATCGTAGTCTGGTGTTAACTCATAACTGGACTAAACTTTATGGGGAAGTAGTTGAA
ATGCGAAAAGCTTGCGGAAATCGTGCTCACTTAAAGACAATATTGGGTATTGGAGAGTGC
GGTACTATGGAGAATGTTTATAAAGCTTCCATGATATGTATGATGGCTGGTGCTGATTTC
ATAAAAACAAGCACTGGAAAAGAGGTTGTTAATGCAACCCTTCCAGTTGGTTTATGTATG
ATTAGAGCAATTCAAGAATTTCATCGTTTAACAAAAAAGAATGTTGGTCTTAAACCAGCT
GGTGGTGTTCGCACTGTAAATGATGCTATAAAATGGATAATTTTAATCAAAGAAACTCTT
GGTATGGAATATCTTCAGCCACATCTCTTTCGCTTTGGTGCTTCTGGTTTACTGGATGAT
ATTGAAAAAGTCGTTAAAAGTAAATGTTAA
>g4950.t1 Gene=g4950 Length=309
MHVNETIPFEQSWIENVNIQLRGLEAAVKLIVSHCHVTSDENIVAFALKALTLTDLTTLA
GDDCESNVERLCVRACYPFFNHSVKNDSNEFYKSLHTAAVCVYPSKVKNAYDTLKRLNML
DKVQIASVATGFPTGLYPLQSRLDEIKYAIENGATEIDIVIDRSLVLTHNWTKLYGEVVE
MRKACGNRAHLKTILGIGECGTMENVYKASMICMMAGADFIKTSTGKEVVNATLPVGLCM
IRAIQEFHRLTKKNVGLKPAGGVRTVNDAIKWIILIKETLGMEYLQPHLFRFGASGLLDD
IEKVVKSKC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4950.t1 | CDD | cd00959 | DeoC | 61 | 281 | 0 |
| 5 | g4950.t1 | Gene3D | G3DSA:3.20.20.70 | Aldolase class I | 40 | 307 | 0 |
| 2 | g4950.t1 | PANTHER | PTHR10889 | DEOXYRIBOSE-PHOSPHATE ALDOLASE | 3 | 306 | 0 |
| 3 | g4950.t1 | PANTHER | PTHR10889:SF3 | DEOXYRIBOSE-PHOSPHATE ALDOLASE | 3 | 306 | 0 |
| 6 | g4950.t1 | PIRSF | PIRSF001357 | DeoC | 44 | 308 | 0 |
| 1 | g4950.t1 | Pfam | PF01791 | DeoC/LacD family aldolase | 52 | 271 | 0 |
| 8 | g4950.t1 | SMART | SM01133 | DeoC_2 | 49 | 303 | 0 |
| 4 | g4950.t1 | SUPERFAMILY | SSF51569 | Aldolase | 44 | 304 | 0 |
| 9 | g4950.t1 | TIGRFAM | TIGR00126 | deoC: deoxyribose-phosphate aldolase | 51 | 281 | 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 transcript has been annotated with K01619 (deoxyribose-phosphate aldolase)
Pathway
- This transcript belongs to the following pathways
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.
