General information for g434.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Rad51.
Parent gene
- The parent gene g434 is located on chr_3: 3341946..3344349 (- 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 | g434 | g434.t4 | TTS | g434.t4 | 3341862 | 3341862 |
| chr_3 | g434 | g434.t4 | isoform | g434.t4 | 3341946 | 3343100 |
| chr_3 | g434 | g434.t4 | exon | g434.t4.exon1 | 3341946 | 3342721 |
| chr_3 | g434 | g434.t4 | cds | g434.t4.CDS1 | 3341946 | 3342428 |
| chr_3 | g434 | g434.t4 | exon | g434.t4.exon2 | 3342777 | 3342940 |
| chr_3 | g434 | g434.t4 | exon | g434.t4.exon3 | 3343002 | 3343100 |
| chr_3 | g434 | g434.t4 | TSS | g434.t4 | 3343167 | 3343167 |
Sequences
>g434.t4 Gene=g434 Length=1039
ATGGCAATGCAAGGTGCTTCAACTAGTGCTAATGCATCCGCAATTAGTCATGATGAAGAT
ACAGATCAAGGAATATTTACACCAATAGCAAAACTTGAGACAATAAATGGAGTTACACCT
GGAGATATTAAAAAGTTGAAGGAAGCAGGATATCATACAGTCGAATCGATTGCATATACA
TTGAAAAAATGCTTGGCTACTGTAAAAGGAATTTCAGAACAAAAAGCTGAAAAATTAATT
GACGAGGCGGGAAAAATGAGTAATTGGACTTGGAATCACATCTGCATCATTAATTCTGAA
ACAAAGAGCCGAACAGATTTCAATTACAACTGGATCACGAGAATTAGATAAATTACTTGG
TGGAGGAATTGAAACAGGTTCGATCACAGAAGTATTTGGTGAATTTCGTTCTGGAAAAAC
TCAACTTGCACACACATTAGCTGTTACTTGTCAATTGCCTGCAAATAGTGGAGGAGGACA
AGGAAAATGCTTATATATTGATACTGAAGGAACATTTAGACCTGAAAGATTGTCATCTAT
AGCCGAACGTTTTAAAATGGATCCAAATGAAGTTCTTGACAATATTGCTGTCGCTCGCGC
TTACAACACAGATCATCAATTAACTCTTCTCGTTCATGCATCTGCAATTATGGCTGATAC
TCGATTTGCCTTACTCGTTGTTGATAGTGCAACTGCTTTATATCGTACAGATTATTCTGG
TCGCGGTGAACTTGCAGCTCGACAAATGCATCTTGCAAAATTTATGCGTCATTTACTTCG
CATGGCTGACGAATTCGGAATCGCTGTATTAATTACCAATCAAGTTGTAGCTAATGTTGA
CAATTCATCCATGTTTGCTGGAGATTCTAAAAAACCAATCGGAGGAAATATCATAGCTCA
TGCATCGACTACACGTTTATATTTACGTAAAGCAAGAGGAGAAAATCGTGTCTGTAAAAT
TTATGATTCACCATCACTACCAGAAGCTGAAGCACAGTTTTCAATTGGAGTTGATGGAAT
TAATGATCCAAAAGAATAA
>g434.t4 Gene=g434 Length=160
MDPNEVLDNIAVARAYNTDHQLTLLVHASAIMADTRFALLVVDSATALYRTDYSGRGELA
ARQMHLAKFMRHLLRMADEFGIAVLITNQVVANVDNSSMFAGDSKKPIGGNIIAHASTTR
LYLRKARGENRVCKIYDSPSLPEAEAQFSIGVDGINDPKE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g434.t4 | CDD | cd01123 | Rad51_DMC1_radA | 1 | 155 | 0.000 |
| 5 | g434.t4 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 160 | 0.000 |
| 2 | g434.t4 | PANTHER | PTHR22942:SF39 | DNA REPAIR PROTEIN RAD51 HOMOLOG 1 | 2 | 160 | 0.000 |
| 3 | g434.t4 | PANTHER | PTHR22942 | RECA/RAD51/RADA DNA STRAND-PAIRING FAMILY MEMBER | 2 | 160 | 0.000 |
| 1 | g434.t4 | Pfam | PF08423 | Rad51 | 1 | 157 | 0.000 |
| 6 | g434.t4 | ProSiteProfiles | PS50162 | RecA family profile 1. | 1 | 90 | 23.827 |
| 7 | g434.t4 | ProSiteProfiles | PS50163 | RecA family profile 2. | 97 | 160 | 19.106 |
| 4 | g434.t4 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 1 | 157 | 0.000 |
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 |
| GO:0006259 | DNA metabolic 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.
