Gene loci information

Transcript annotation

  • This transcript has been annotated as Rad51.

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_3 g434 g434.t6 TTS g434.t6 3341862 3341862
chr_3 g434 g434.t6 isoform g434.t6 3341946 3344349
chr_3 g434 g434.t6 exon g434.t6.exon1 3341946 3342721
chr_3 g434 g434.t6 cds g434.t6.CDS1 3341946 3342721
chr_3 g434 g434.t6 exon g434.t6.exon2 3342781 3342940
chr_3 g434 g434.t6 cds g434.t6.CDS2 3342781 3342940
chr_3 g434 g434.t6 exon g434.t6.exon3 3343002 3343120
chr_3 g434 g434.t6 cds g434.t6.CDS3 3343002 3343100
chr_3 g434 g434.t6 exon g434.t6.exon4 3344043 3344349
chr_3 g434 g434.t6 TSS g434.t6 NA NA

Sequences

>g434.t6 Gene=g434 Length=1362
TTTTCTTTTGTGTGTTGTCGGCGAATTTTGTTTACAAAACAAACTGCTATATCGCTATAT
TAATTTTAATTCGTTGAATATTTTTCGTAAAAGCGCATTAAAATGTTTCTTGTTTCACTC
TTTGAATGAATTTATAGTGCAAAACAAGAGAATTTCACTATTCACTTATATTTTTAATAA
ATTTAAACTTTCAATTTAAAGAGATATATAGTCTTCTTTCAATAATTTTAACACTACAGC
TGTTTTTAAAATATCGATAAAGCAATTTACACAAGGGGATATTCACTGGTGCGAAGAATT
TTAAAATATTTTAAAAACTAAAGTAAAATGGCAATGCAAGGTGCTTCAACTAGTGCTAAT
GCATCCGCAATTAGTCATGATGAAGATACAGATCAAGGAATATTTACACCAATAGCAAAA
CTTGAGACAATAAATGGAGTTACACCTGGAGATATTAAAAAGTTGAAGGAAGCAGGATAT
CATACAGTCGAATCGATTGCATATACATTGAAAAAATGCTTGGCTACTGTAAAAGGAATT
TCAGAACAAAAAGCTGAAAAATTAATTGACGAGGCGGGAAAAATGATTGGACTTGGAATC
ACATCTGCATCATTAATTCTGAAACAAAGAGCCGAACAGATTTCAATTACAACTGGATCA
CGAGAATTAGATAAATTACTTGGTGGAGGAATTGAAACAGGTTCGATCACAGAAGTATTT
GGTGAATTTCGTTCTGGAAAAACTCAACTTGCACACACATTAGCTGTTACTTGTCAATTG
CCTGCAAATAGTGGAGGAGGACAAGGAAAATGCTTATATATTGATACTGAAGGAACATTT
AGACCTGAAAGATTGTCATCTATAGCCGAACGTTTTAAAATGGATCCAAATGAAGTTCTT
GACAATATTGCTGTCGCTCGCGCTTACAACACAGATCATCAATTAACTCTTCTCGTTCAT
GCATCTGCAATTATGGCTGATACTCGATTTGCCTTACTCGTTGTTGATAGTGCAACTGCT
TTATATCGTACAGATTATTCTGGTCGCGGTGAACTTGCAGCTCGACAAATGCATCTTGCA
AAATTTATGCGTCATTTACTTCGCATGGCTGACGAATTCGGAATCGCTGTATTAATTACC
AATCAAGTTGTAGCTAATGTTGACAATTCATCCATGTTTGCTGGAGATTCTAAAAAACCA
ATCGGAGGAAATATCATAGCTCATGCATCGACTACACGTTTATATTTACGTAAAGCAAGA
GGAGAAAATCGTGTCTGTAAAATTTATGATTCACCATCACTACCAGAAGCTGAAGCACAG
TTTTCAATTGGAGTTGATGGAATTAATGATCCAAAAGAATAA

>g434.t6 Gene=g434 Length=344
MAMQGASTSANASAISHDEDTDQGIFTPIAKLETINGVTPGDIKKLKEAGYHTVESIAYT
LKKCLATVKGISEQKAEKLIDEAGKMIGLGITSASLILKQRAEQISITTGSRELDKLLGG
GIETGSITEVFGEFRSGKTQLAHTLAVTCQLPANSGGGQGKCLYIDTEGTFRPERLSSIA
ERFKMDPNEVLDNIAVARAYNTDHQLTLLVHASAIMADTRFALLVVDSATALYRTDYSGR
GELAARQMHLAKFMRHLLRMADEFGIAVLITNQVVANVDNSSMFAGDSKKPIGGNIIAHA
STTRLYLRKARGENRVCKIYDSPSLPEAEAQFSIGVDGINDPKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g434.t6 CDD cd01123 Rad51_DMC1_radA 107 339 0.0000000
8 g434.t6 Gene3D G3DSA:1.10.150.20 5’ to 3’ exonuclease 1 90 0.0000000
7 g434.t6 Gene3D G3DSA:3.40.50.300 - 99 344 0.0000000
3 g434.t6 PANTHER PTHR22942:SF39 DNA REPAIR PROTEIN RAD51 HOMOLOG 1 16 344 0.0000000
4 g434.t6 PANTHER PTHR22942 RECA/RAD51/RADA DNA STRAND-PAIRING FAMILY MEMBER 16 344 0.0000000
9 g434.t6 PIRSF PIRSF005856 Rad51 15 344 0.0000000
2 g434.t6 Pfam PF14520 Helix-hairpin-helix domain 31 85 0.0000000
1 g434.t6 Pfam PF08423 Rad51 90 341 0.0000000
13 g434.t6 ProSiteProfiles PS50162 RecA family profile 1. 103 274 51.3380000
14 g434.t6 ProSiteProfiles PS50163 RecA family profile 2. 281 344 19.1060000
11 g434.t6 SMART SM00382 AAA_5 124 311 0.0000005
5 g434.t6 SUPERFAMILY SSF47794 Rad51 N-terminal domain-like 24 87 0.0000000
6 g434.t6 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 107 341 0.0000000
12 g434.t6 TIGRFAM TIGR02239 recomb_RAD51: DNA repair protein RAD51 31 344 0.0000000

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:0006259 DNA metabolic process BP
GO:0003690 double-stranded DNA binding MF
GO:0000150 DNA strand exchange activity MF
GO:0003697 single-stranded DNA binding MF
GO:0000166 nucleotide binding MF
GO:0008094 ATP-dependent activity, acting on DNA MF
GO:0000724 double-strand break repair via homologous recombination BP
GO:1990426 mitotic recombination-dependent replication fork processing BP

KEGG

Orthology

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.

Raw TPM values