RetrogeneDB ID: retro_brap_48

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A07:21989549..21990623(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra010092
• Aliases: None
• Description: None

Sequence

>retro_brap_48
ATGGATACAGCCGGAGTGAAACGTGCTCGCTACACTAGCCCGCCTGGTGAAGTTGATCGGCTAAGCAGTTTGCCAGATTG
CTTGATATTCCATGTACTCTTAAATCTTCCGACCAAAGATGTGGTTCAGACCAGTCTCTTATCCCCCAGATGGACACATC
TCTGGAAACACGTACCTGGTCTAGACTTAGACACCGAAGATTTCAAAGAACTTGACACCTTCGTGACTGTTGTCGATAGC
TTTCTTGAACGTAACCGCGGTTCGTCCGTACATTGTTTTAAGTTAGCGTACGACTCTCCCGTCGTTGTTGAGCCTAACAC
TGGTCTTGTCAAGCGCTGGCTCGACGCTGCTGCTAAGCTGAAAGTTAAACATCTCAATGTTTCGGACAATTCATCACAGA
GTTGGGACCTCGTGATGTCTCCAACGGTTTACACCTGTAGCAGCTTGGTATCCTTAAGGCTCGTGGGGCTAACCTTACCT
AATACCGAGAGTGTTTCATTACCTTCTCTCAAAGCTATGGTTTTACTCCTCGTTGAGTTTACCAACAATCGGGCATTAGA
GAATTTAATCTCAAAATGTCCAGTTCTTGAAAACTTATGTATTGAGAGAAGCTACGGTGATGGAATATCGATTTTACGTG
TGCATTCTAAGTCTCTGTTGACCTTCATGCATGATGCGGGTAATAACGAGGATTATGATGAAGATCGTATAGTTGAAATC
GATGCTCCCATGCTTATTTATCTGAGGATCAGTGATGCTCGAACTACAAGTTTCATAATAAAGAGTCCACCTTCCATTGT
GGAAGCGGATATAGATACTGTGTTTAACTTAATTTCTGGAAGGAGACTAGGAGTTGCAAATGAAGTACAAAAGAGAGAGA
TGGTTCGTGATTTTCTCATTGGGATCTCTAATGTGAAAGATCTGACCATAGCCTCCTCTACTCTCGAGGTAACCTTAAGA
CATTATTTGAATGCTGAAAACTTAAAACCAATTATCTATAAAATAAATTGATTTTTTTATATTTTAGTTAATTATTCTCT
AACTACCGATATAAGACTTTATTTATTAGTACTA

Alignment

ORF - retro_brap_48 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 87.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDAARVKPARSTNPPSEVDRLSSLPDCLILQIFLNLPTKDVVQTSALSTRWTTLWKDVSGLDLDAEDFYI
          MD.A.VK.AR.T.PP.EVDRLSSLPDCLI....LNLPTKDVVQTS.LS.RWT.LWK.V.GLDLD.EDF..
Retrocopy MDTAGVKRARYTSPPGEVDRLSSLPDCLIFHVLLNLPTKDVVQTSLLSPRWTHLWKHVPGLDLDTEDFKE

Parental  RETFVSFFDNFLERNHGLSIHRFKLKYDSFYFEEP-AGLINGWVDTAARLKVEHLDVSDSFSE-WDPMMN
          ..TFV...D.FLERN.G.S.H.FKL.YDS....EP..GL...W.D.AA.LKV.HL.VSD..S..WD..M.
Retrocopy LDTFVTVVDSFLERNRGSSVHCFKLAYDSPVVVEPNTGLVKRWLDAAAKLKVKHLNVSDNSSQSWDLVMS

Parental  PTVLYTCSNLVSLRLVGMGLPNPERVSLPSLKTVVLILIEFTNKWALENLISKCPVLENFCFERSYDDGI
          PTV.YTCS.LVSLRLVG..LPN.E.VSLPSLK..VL.L.EFTN..ALENLISKCPVLEN.C.ERSY.DGI
Retrocopy PTV-YTCSSLVSLRLVGLTLPNTESVSLPSLKAMVLLLVEFTNNRALENLISKCPVLENLCIERSYGDGI

Parental  PILRVHSKSLLTFMHDAGYHEDYEEEDRFVEIDAPMLKCLKISDDRTSSFIIKSPPSVVEADIDTVFNLT
          .ILRVHSKSLLTFMHDAG..EDY..EDR.VEIDAPML..L.ISD.RT.SFIIKSPPS.VEADIDTVFNL.
Retrocopy SILRVHSKSLLTFMHDAGNNEDY-DEDRIVEIDAPMLIYLRISDARTTSFIIKSPPSIVEADIDTVFNLI

Parental  SERSLGIANEVQKREMVRDFLVGISKVKDMSISSSALEVPM-SYMIMQDMYHYRYFVTYIPCVSVGYLLE
          S.R.LG.ANEVQKREMVRDFL.GIS.VKD..I.SS.LEV....Y..........Y.........V.Y.L.
Retrocopy SGRRLGVANEVQKREMVRDFLIGISNVKDLTIASSTLEVTLRHYLNAENLKPIIYKIN*XXXILVNYSLT

Parental  NSPNLKKLSL
          ....L..L.L
Retrocopy TDIRLYLLVL

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_48 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	Bra010092	1 retrocopy	retro_brap_48 ,