RetrogeneDB ID: retro_brap_31

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A01:21478888..21479290(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra038226
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra028263
• Aliases: None
• Description: None

Sequence

>retro_brap_31
ATGGCTTACGCACCACCAACGAAGCAAGGAAAGACTGAATTTGAGAAGCCACAAGAGCAGATTCACAAGATCGGAATCAC
TCTCTCCTCAAAGAACGTCAAAAACCTTGAGAAGGTGTGCACTGACTTGGTCCGTGGTGCCAAAGACAAGAGATTGAGAG
TGAAAGGACCAGTGAGGATGCCAACTAAAGTTCTCAAAGTTACCACAAGAAAAGCTCCTTGTGGTGAAGGAAACAACACA
TGGGACAGGTTCGAGCTCCGTGTACACAAGCGTGTGATCGATCTCTTCAGCTCTCCTGATGTTGTGAAGCAGATCACTTC
CATCACCATTGAGCCTGGTGTTGAGGTCGAGGTCACCATTGCTGATTCATTCATGCGCTTTAATTCACAATCTTGTCTTT
GA

Alignment

ORF - retro_brap_31 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.12 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAYAPPMKQGKTGFEEPQEQIHKIRITLSSKNVKNLEKVCTDLVRGAKDKRLRVKGPVRMPTKVLKITTR
          MAYAPP.KQGKT.FE.PQEQIHKI.ITLSSKNVKNLEKVCTDLVRGAKDKRLRVKGPVRMPTKVLK.TTR
Retrocopy MAYAPPTKQGKTEFEKPQEQIHKIGITLSSKNVKNLEKVCTDLVRGAKDKRLRVKGPVRMPTKVLKVTTR

Parental  KAPCGEGTNTWDRFELRVHKRVIDLFSSPDVVKQITSITIEPGVEVEVTIADS
          KAPCGEG.NTWDRFELRVHKRVIDLFSSPDVVKQITSITIEPGVEVEVTIADS
Retrocopy KAPCGEGNNTWDRFELRVHKRVIDLFSSPDVVKQITSITIEPGVEVEVTIADS

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_31 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica rapa	Bra028263	1 retrocopy	retro_brap_31 ,
Physcomitrella patens	PP1S257_105V6	1 retrocopy	retro_ppat_38,