RetrogeneDB ID: retro_brap_18

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A09:27260899..27261655(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra007092
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra037306
• Aliases: None
• Description: None

Sequence

>retro_brap_18
ATGATGAGCTTCCTAAGGAGATCCATCGGCAGCCTATCCAAATCGACCCTCCAGTTTACCTCCGCTTCACAAACAGGAGC
ATCAAGTCAAGCCATTCCCGATTCTGGTCTCATGAGTGTGGTCTCAAATGGAGCTAAGGGACTCTTCTTTGGCTTCCGAC
GTATGGAATCTTGTCCAATGAACATCAGCAGGCCCTCTTGCTTGTTGTCTAGATCTTTTGCGTCGAGAACTTCCAAGGAA
CCTGCTAAGAAAGAGGTGGTGACTGTGGAGGAGGATCCTTTTGATTCTCCGACGTACCATATCCCGGAGAAGCCGGTAAC
CTTTACAGAAGGTGCTTCCTACAGTTTTGTTATCCTGGCCGGGCTTGCGGTCGCTGGGGCTTCTGGGTACGCTGTGTTTA
AAGAGCTCGTGTTTCAACCAAAAGAGTACAAGGTCTTTGACAAAGCGTTTAAGAGAATCCAAGATGACGGTCAGGTGAGG
GTGAGGATTGGATCCCCCATCACAGGGTACGGACAAGAAACCAGAAACCGAGCTGCTCGCCAACGTATACCGAACAGAGT
GTTTACAGATGAAGAGGGAGTGGAGCATGTGGAGGTAAACTTCTTCATCCGTGGGCCTCATGGAGCCGGGAAAGTGTACA
CGGAGATGTTTAAAGACAAGGCAGATAAGAAGGAATGGAAATACACATACCTGATCGTTGAGATTTTAGCTCCCTCCCCA
GCCAAACTGATGCTGGAGTCCTATTTGCCCGCCTAG

Alignment

ORF - retro_brap_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.88 %
• Parental protein coverage: 56. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AKKEVVTVE-DPFDSPTYHIPEKPVTFTEGASYSFVILAGLAVAGASGHAAFKELIFQPKEYKVFDKALK
          AKKEVVTVE.DPFDSPTYHIPEKPVTFTEGASYSFVILAGLAVAGASG.A.FKEL.FQPKEYKVFDKA.K
Retrocopy AKKEVVTVEEDPFDSPTYHIPEKPVTFTEGASYSFVILAGLAVAGASGYAVFKELVFQPKEYKVFDKAFK

Parental  RIQDDGQVRVRIGSPITGYGQETRNRAARQRIPNRVFTDEDGVEHVEVNFFIRGPHGAGKVYTEMFKDKA
          RIQDDGQVRVRIGSPITGYGQETRNRAARQRIPNRVFTDE.GVEHVEVNFFIRGPHGAGKVYTEMFKDKA
Retrocopy RIQDDGQVRVRIGSPITGYGQETRNRAARQRIPNRVFTDEEGVEHVEVNFFIRGPHGAGKVYTEMFKDKA

Parental  D-KEWKYTYLIVEILAPSPAKLMLESYLPA
          D.KEWKYTYLIVEILAPSPAKLMLESYLPA
Retrocopy DKKEWKYTYLIVEILAPSPAKLMLESYLPA

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_18 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Brassica rapa	Bra037306	1 retrocopy	retro_brap_18 ,