RetrogeneDB ID:

retro_brap_28

Retrocopy
location
Organism:Chinese cabbage (Brassica rapa)
Coordinates:A09:32502910..32503279(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:Bra031095
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:Bra009348
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_brap_28
ATGATGGTGGAGACCTCTGAAAGAAGCAGTTCGTTGGATGTTGCAATAGATTCTTCAAACATAGGGTTTAAGCTTCTAAA
GAAGCAAGGGTGGAAGGAAGGCACTGGTCTTGGAATCTCTCAACAGGGTATATTAGAGCCTCTGCAAACATTGCTCAAAA
ATAACAAACGAGGACTTGGAGCTGAAATTACAACTAAGAGAAAAGCGGCAAAGCCTCATCACTCTATTGCTACAGATTCT
AAACAAGTCGCTAAGAAAGCAAAGAAACTGTCTAAGAAGATGCGGAAGATGATCGAGCACGAGAAACACTTGCTGGAAAA
GGAATTTGAACGAGCTTTCTTTAGAGAGTTCTGGCCTGATAATGTATAA

ORF - retro_brap_28 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.07 %
Parental protein coverage: 97.52 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSAGSSSSWAAINSSNIGFQLLKKQGWKEGTGLGVAEQGILVPVQAELKNNKRGIGAVAEKPTKRKAVKAS
S..SSS...AI.SSNIGF.LLKKQGWKEGTGLG...QGIL.P.Q..LKNNKRG.G..AE..TKRKA.K..
RetrocopySERSSSLDVAIDSSNIGFKLLKKQGWKEGTGLGISQQGILEPLQTLLKNNKRGLG--AEITTKRKAAKPH
ParentalTDSGKE-EEVSKQSKKLSKKMRKLMEHEKQLQEKEFERAFFREFWPDNV
.........V.K..KKLSKKMRK..EHEK.L.EKEFERAFFREFWPDNV
RetrocopyHSIATDSKQVAKKAKKLSKKMRKMIEHEKHLLEKEFERAFFREFWPDNV

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Brassica rapa was not studied using RNA-Seq expression data.
Brassica rapa was not studied using ChIP-Seq data.
Brassica rapa was not studied using EST data.
Brassica rapa was not studied using FANTOM5 data.
retro_brap_28 was not experimentally validated.

Retrocopy orthology:
Brassica rapa does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Brassica oleracea Bo9g1743601 retrocopy
Brassica rapa Bra009348 1 retrocopy
retro_brap_28 ,
Arabidopsis lyrata fgenesh1_pg.C_scaffold_60007121 retrocopy



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