General information for g2680.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA repair protein RAD51 homolog 1.
Parent gene
- The parent gene g2680 is located on chr_3: 19693023..19693771 (- 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_3 | g2680 | g2680.t1 | TTS | g2680.t1 | 19692652 | 19692652 |
| chr_3 | g2680 | g2680.t1 | isoform | g2680.t1 | 19692711 | 19693771 |
| chr_3 | g2680 | g2680.t1 | exon | g2680.t1.exon1 | 19692711 | 19693517 |
| chr_3 | g2680 | g2680.t1 | cds | g2680.t1.CDS1 | 19692711 | 19693517 |
| chr_3 | g2680 | g2680.t1 | exon | g2680.t1.exon2 | 19693583 | 19693771 |
| chr_3 | g2680 | g2680.t1 | cds | g2680.t1.CDS2 | 19693583 | 19693771 |
| chr_3 | g2680 | g2680.t1 | TSS | g2680.t1 | 19693817 | 19693817 |
Sequences
>g2680.t1 Gene=g2680 Length=996
ATGACCTCAAGTAGCAGCAATAAATCTTCTCAGGATAATGTGATATTCAGTGATGATGAT
AGTCTTCAATTGTTTATTAGAGAAAGTGAACTTCAAGAAACATCTTTTAAAGAAAACGAC
AAAATTATTGAAGATGAAGAGATTTTAAGAAATGAAAAAAATCATAATCCGAGAAAAAGG
AAATTTGAGGTTCCTTTAGAACTTAATGATGAAGAACTCCCTTTTAAATTCGATGCAGAA
AGATTATTTTTTTCTGAATCGAATGAAGAAATTGAAAAGAATTCGATAACTACTGGGTCA
CGAACAATAGATAAGCTACTTGAAGGCGGTATAGAAGTTGGCTCTATTACAGAATTATTT
GGCGAATCGCGTACAGGAAAAACACAGTTTGTACACACATTGGCTGTTACATGTCAATTA
CCGATTGATTCTGGTGGAGGTGGAGGAAAGTGTTTGTTTATCGATACTGAAGGAACTTTT
AGACCTGAGAGATTATTAACTATAGCTCAACGTTTTGGGATGAATCCTGAAGAGGTTCTT
GATAATGTGCACTATGTGCGCGTCTATAATACCGAGCATCAAAAGAAAATTCTTGATAAA
GCTCGTTCATTAATGCTTCAAAACCAATTTGCACTAATTGTTGTCGACTGTGTTACTTCT
TTGTATCGTACTGATTTTCCTGAAGTTGAAGAAATTTTGATACGACATAAGCATTTAAAA
AGCTTTTTACGACGGCTACAAAATTTGATATACGAATATAACATTGCAGCCGTAGTTACT
AATCAAATTTCATCATATCCGAAAGGTCCTACGAAGACTATTACAAAACCTTTTGCAAAT
AGTACAATTGGACATTCATCAACAACACGTCTTTATTTAAAAAATTACCTCAACAACACT
CGTATTTGTCAAATATATAGTTCTCCCTCATTACCAGAATGTTCTGTTTTTTATTCAATT
AACAATGGTGGTATCACAGATGCAAAAGATAATTAA
>g2680.t1 Gene=g2680 Length=331
MTSSSSNKSSQDNVIFSDDDSLQLFIRESELQETSFKENDKIIEDEEILRNEKNHNPRKR
KFEVPLELNDEELPFKFDAERLFFSESNEEIEKNSITTGSRTIDKLLEGGIEVGSITELF
GESRTGKTQFVHTLAVTCQLPIDSGGGGGKCLFIDTEGTFRPERLLTIAQRFGMNPEEVL
DNVHYVRVYNTEHQKKILDKARSLMLQNQFALIVVDCVTSLYRTDFPEVEEILIRHKHLK
SFLRRLQNLIYEYNIAAVVTNQISSYPKGPTKTITKPFANSTIGHSSTTRLYLKNYLNNT
RICQIYSSPSLPECSVFYSINNGGITDAKDN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g2680.t1 | CDD | cd01123 | Rad51_DMC1_radA | 96 | 325 | 0.00000 |
| 5 | g2680.t1 | Gene3D | G3DSA:3.40.50.300 | - | 94 | 330 | 0.00000 |
| 2 | g2680.t1 | PANTHER | PTHR22942 | RECA/RAD51/RADA DNA STRAND-PAIRING FAMILY MEMBER | 93 | 330 | 0.00000 |
| 1 | g2680.t1 | Pfam | PF08423 | Rad51 | 94 | 328 | 0.00000 |
| 6 | g2680.t1 | ProSiteProfiles | PS50162 | RecA family profile 1. | 92 | 263 | 42.73800 |
| 4 | g2680.t1 | SMART | SM00382 | AAA_5 | 113 | 297 | 0.00031 |
| 3 | g2680.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 95 | 328 | 0.00000 |
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:0003677 | DNA binding | MF |
| GO:0006281 | DNA repair | BP |
| GO:0005524 | ATP binding | MF |
| GO:0008094 | ATP-dependent activity, acting on DNA | 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.
