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.t5 TTS g434.t5 3341862 3341862
chr_3 g434 g434.t5 isoform g434.t5 3341946 3343100
chr_3 g434 g434.t5 exon g434.t5.exon1 3341946 3342721
chr_3 g434 g434.t5 cds g434.t5.CDS1 3341946 3342721
chr_3 g434 g434.t5 exon g434.t5.exon2 3342781 3343100
chr_3 g434 g434.t5 cds g434.t5.CDS2 3342781 3342784
chr_3 g434 g434.t5 TSS g434.t5 3343167 3343167

Sequences

>g434.t5 Gene=g434 Length=1096
ATGGCAATGCAAGGTGCTTCAACTAGTGCTAATGCATCCGCAATTAGTCATGATGAAGAT
ACAGATCAAGGAATATTTACACCAATAGCAAAACTTGAGGTAAATTTAAATTTTTTGAAT
TCGAAACGAATTTCATAATAAAATGTTTGTCCAAATGTAGACAATAAATGGAGTTACACC
TGGAGATATTAAAAAGTTGAAGGAAGCAGGATATCATACAGTCGAATCGATTGCATATAC
ATTGAAAAAATGCTTGGCTACTGTAAAAGGAATTTCAGAACAAAAAGCTGAAAAATTAAT
TGACGAGGCGGGAAAAATGATTGGACTTGGAATCACATCTGCATCATTAATTCTGAAACA
AAGAGCCGAACAGATTTCAATTACAACTGGATCACGAGAATTAGATAAATTACTTGGTGG
AGGAATTGAAACAGGTTCGATCACAGAAGTATTTGGTGAATTTCGTTCTGGAAAAACTCA
ACTTGCACACACATTAGCTGTTACTTGTCAATTGCCTGCAAATAGTGGAGGAGGACAAGG
AAAATGCTTATATATTGATACTGAAGGAACATTTAGACCTGAAAGATTGTCATCTATAGC
CGAACGTTTTAAAATGGATCCAAATGAAGTTCTTGACAATATTGCTGTCGCTCGCGCTTA
CAACACAGATCATCAATTAACTCTTCTCGTTCATGCATCTGCAATTATGGCTGATACTCG
ATTTGCCTTACTCGTTGTTGATAGTGCAACTGCTTTATATCGTACAGATTATTCTGGTCG
CGGTGAACTTGCAGCTCGACAAATGCATCTTGCAAAATTTATGCGTCATTTACTTCGCAT
GGCTGACGAATTCGGAATCGCTGTATTAATTACCAATCAAGTTGTAGCTAATGTTGACAA
TTCATCCATGTTTGCTGGAGATTCTAAAAAACCAATCGGAGGAAATATCATAGCTCATGC
ATCGACTACACGTTTATATTTACGTAAAGCAAGAGGAGAAAATCGTGTCTGTAAAATTTA
TGATTCACCATCACTACCAGAAGCTGAAGCACAGTTTTCAATTGGAGTTGATGGAATTAA
TGATCCAAAAGAATAA

>g434.t5 Gene=g434 Length=259
MIGLGITSASLILKQRAEQISITTGSRELDKLLGGGIETGSITEVFGEFRSGKTQLAHTL
AVTCQLPANSGGGQGKCLYIDTEGTFRPERLSSIAERFKMDPNEVLDNIAVARAYNTDHQ
LTLLVHASAIMADTRFALLVVDSATALYRTDYSGRGELAARQMHLAKFMRHLLRMADEFG
IAVLITNQVVANVDNSSMFAGDSKKPIGGNIIAHASTTRLYLRKARGENRVCKIYDSPSL
PEAEAQFSIGVDGINDPKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g434.t5 CDD cd01123 Rad51_DMC1_radA 22 254 1.56292E-140
5 g434.t5 Gene3D G3DSA:3.40.50.300 - 14 259 4.1E-87
2 g434.t5 PANTHER PTHR22942:SF39 DNA REPAIR PROTEIN RAD51 HOMOLOG 1 4 259 9.6E-129
3 g434.t5 PANTHER PTHR22942 RECA/RAD51/RADA DNA STRAND-PAIRING FAMILY MEMBER 4 259 9.6E-129
11 g434.t5 PIRSF PIRSF003336 RadB 16 258 1.2E-46
1 g434.t5 Pfam PF08423 Rad51 5 256 3.5E-122
7 g434.t5 Phobius SIGNAL_PEPTIDE Signal peptide region 1 17 -
8 g434.t5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 1 -
9 g434.t5 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 2 13 -
10 g434.t5 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 14 17 -
6 g434.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 18 259 -
14 g434.t5 ProSiteProfiles PS50162 RecA family profile 1. 18 189 51.338
15 g434.t5 ProSiteProfiles PS50163 RecA family profile 2. 196 259 19.106
13 g434.t5 SMART SM00382 AAA_5 39 226 5.3E-7
4 g434.t5 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 22 256 2.13E-60

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:0003684 damaged DNA binding MF
GO:0008094 ATP-dependent activity, acting on DNA MF
GO:0006310 DNA recombination BP
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.

Raw TPM values