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 symbol: None
• Ensembl ID: Bra009348
• Aliases: None
• Description: None

Sequence

>retro_brap_28
ATGATGGTGGAGACCTCTGAAAGAAGCAGTTCGTTGGATGTTGCAATAGATTCTTCAAACATAGGGTTTAAGCTTCTAAA
GAAGCAAGGGTGGAAGGAAGGCACTGGTCTTGGAATCTCTCAACAGGGTATATTAGAGCCTCTGCAAACATTGCTCAAAA
ATAACAAACGAGGACTTGGAGCTGAAATTACAACTAAGAGAAAAGCGGCAAAGCCTCATCACTCTATTGCTACAGATTCT
AAACAAGTCGCTAAGAAAGCAAAGAAACTGTCTAAGAAGATGCGGAAGATGATCGAGCACGAGAAACACTTGCTGGAAAA
GGAATTTGAACGAGCTTTCTTTAGAGAGTTCTGGCCTGATAATGTATAA

Alignment

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:

Parental  SAGSSSSWAAINSSNIGFQLLKKQGWKEGTGLGVAEQGILVPVQAELKNNKRGIGAVAEKPTKRKAVKAS
          S..SSS...AI.SSNIGF.LLKKQGWKEGTGLG...QGIL.P.Q..LKNNKRG.G..AE..TKRKA.K..
Retrocopy SERSSSLDVAIDSSNIGFKLLKKQGWKEGTGLGISQQGILEPLQTLLKNNKRGLG--AEITTKRKAAKPH

Parental  TDSGKE-EEVSKQSKKLSKKMRKLMEHEKQLQEKEFERAFFREFWPDNV
          .........V.K..KKLSKKMRK..EHEK.L.EKEFERAFFREFWPDNV
Retrocopy HSIATDSKQVAKKAKKLSKKMRKMIEHEKHLLEKEFERAFFREFWPDNV

Legend:

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

Expression

RNA-Seq

Brassica rapa was not studied using RNA-Seq expression data.

ChIP-Seq

Brassica rapa was not studied using ChIP-Seq data.

EST

Brassica rapa was not studied using EST data.

TSS

Brassica rapa was not studied using FANTOM5 data.

Lab

retro_brap_28 was not experimentally validated.

Homology

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.

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo9g174360	1 retrocopy	retro_bole_19,
Brassica rapa	Bra009348	1 retrocopy	retro_brap_28 ,
Arabidopsis lyrata	fgenesh1_pg.C_scaffold_6000712	1 retrocopy	retro_alyr_2,