RetrogeneDB ID: retro_brap_17

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A01:9403015..9404047(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra026420
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra028950
• Aliases: None
• Description: None

Sequence

>retro_brap_17
ATGAGTACACGTTATTCAACTCAACTGCAATCATCAGCCATTACATCCATCACCGTCTCCTCATCTTCCTCCTTAGACAC
CACCACTCCACGAGATGATGATAACACTCGCATGTCTCCAGCTTCCAACGCTCGCGTCAACTCTCCAACGTCCTTCTTGA
TAAGACTTGCAATGAGGGTATCTAGAGCAAGGTGGTTCATTTTCTTGAGAAGAGTGTTTCATTACCAGAATGGTTCAAGA
TCCGATCTTGGCGCCAACCCTTTTGAGTCAACCACTTGGATGATATCAGAGCTCATCGCTTTACTCGTACAGATCACTGT
GATCACATTCACACTAGCTTTGTCCAAGAACGAGCGGCCTATTTGGCCCGTGAGGCTCTGGATCACCGGGTACAACGTTG
GATGTTTACTCAGTCTGATGATCTTATACGGTCGGTACCGTCAGCAAGACGTTAGCCAAGGCAATGGGTTTACCTTTGGT
GATATTGAGCAGCAGCAACAGAGAAGCAGAGAAGAGACCAGGTGCTCGCATTTGATGAACAGATGCAGGACATTGCTGGA
GCTCTTCTTTGCGATATGGTTTGTGATAGGAAACGTATGGGTGTTTGATTCTCGGTTCGGTTCTTTCCACTATGCTCCAA
CCCTTCATGTTCTCTGCATCTCCCTTCTCGCTTGGAACGCTCTCTGCTACTCCTTCCCGTTTCTTCTCTTCCTCCTGCTA
TGTTGTGTTGTGCCTCTCATCAGTAGCTTCCTAGGCTACAACATGAACATTGGATCCTCGGAGAAAGGAGCTTCAGATGA
CCAAATCTCTAGTCTCCCAAGCTGGAAGTACAAACTCATCGACGAAACATCTGATTCTGATTCTTCTCACGCAAGCAATG
ATCCGGAGTGTTGCATATGTTTGGCCAAGTATAAAGATAAAGAAGAAGTGAGAAAGCTACCATGTTCTCATAGGTTTCAT
GTAAAATGCGTAGATCAATGGCTTCGTATCATCTCCTCTTGTCCTCTCTGCAAACAAGATCTCCCTAACTAA

Alignment

ORF - retro_brap_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.44 %
• Parental protein coverage: 99.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMSELIALLVQLTVITLTLAISKEERPVWPVRLWITGYDVGCLLSLMLLYGRFRQ--LNQGNWFV--DIE
          M.SELIALLVQ.TVIT.TLA.SK.ERP.WPVRLWITGY.VGCLLSLM.LYGR.RQ....QGN.F...DIE
Retrocopy MISELIALLVQITVITFTLALSKNERPIWPVRLWITGYNVGCLLSLMILYGRYRQQDVSQGNGFTFGDIE

Parental  QQH-RGRDETRSSHLMNKCRTSLELFFAIWFVVGNVWVFDSRFGSFNHAPKLHVLCVSLLSWNALCYSFP
          QQ..R.R.ETR.SHLMN.CRT.LELFFAIWFV.GNVWVFDSRFGSF..AP.LHVLC.SLL.WNALCYSFP
Retrocopy QQQQRSREETRCSHLMNRCRTLLELFFAIWFVIGNVWVFDSRFGSFHYAPTLHVLCISLLAWNALCYSFP

Parental  FLLFLFLCCLVPLISSLLGYNMNMGSSDRGASDDQISSLPSWKHKRADDNA-SDSAPKTDDPECCICLAK
          FLLFL.LCC.VPLISS.LGYNMN.GSS..GASDDQISSLPSWK.K..D....SDS.....DPECCICLAK
Retrocopy FLLFLLLCCVVPLISSFLGYNMNIGSSEKGASDDQISSLPSWKYKLIDETSDSDSSHASNDPECCICLAK

Parental  YKDKEEVRKLPCSHKFHLKCVDQWLRIISCCPLCKQDL
          YKDKEEVRKLPCSH.FH.KCVDQWLRIIS.CPLCKQDL
Retrocopy YKDKEEVRKLPCSHRFHVKCVDQWLRIISSCPLCKQDL

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_17 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 oleracea	Bo3g021260	1 retrocopy	retro_bole_25,
Brassica rapa	Bra028950	1 retrocopy	retro_brap_17 ,