RetrogeneDB ID: retro_brap_7

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A02:22138952..22139951(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra032979
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra014962
• Aliases: None
• Description: None

Sequence

>retro_brap_7
ATGCCTTCCATGGCAGAAGAGCCGCTCCTAACCCCAACCCCAGACAGATTCTGCATGTTCCCGATCCACTACCCTCAGAT
CTGGGAGATGTACAAGAAAGCCGAAGCCTCCTTCTGGACCGCCGAGGAAGTCGACCTCTCCCAAGACACCCGCGACTGGG
AGACCAACCTCAACGACGGCGAGCGCCACTTCATCAAACACGTCCTCGCCTTCTTCGCCGCCTCCGACGGAATCGTCCTC
GAGAATCTCGCCTCCCGGTTCATGTCCGACGTGCAGGTCTCCGAGGCGCGTGCCTTCTACGGGTTCCAGATCGCGATTGA
GAATATCCACTCGGAGATGTACAGCCTCTTGCTAGATACCTACATCAAGGACAACAAGGAGAGGGACCATCTCTTCCGCG
CGATTGAGACCATCCCTTGCGTCGCGAAGAAGGCCCAATGGGCCTTGAAGTGGATCGATGGATCTCAGACTTTCGCAGAG
AGGATCGTGGCCTTCGCGTGCGTGGAAGGGATCTTCTTCTCCGGAAGCTTCTGCTCCATCTTCTGGCTCAAGAAGCGAGG
GCTCATGCCGGGGCTCACCTTCTCCAACGAGCTGATCTCGCGGGACGAAGGCCTTCACTGCGACTTCGCGTGCCTGATCT
ATACCTTGTTGAGGACGAAGCTATCGGAGGAGCGCGTGAAGTCGATCGTGTGCGACGCGGTGGAGATCGAGAGGGAGTTT
GTGTGCGACGCGCTTCCCTGCGCGTTGGTGGGGATGAACCGGGACTTGATGAGTCAGTATATTGAGTTTGTGGCGGATAG
GCTTTTGGGTGCGCTTGGGTACGGGAAGGTGTACGGTGTGGCGAATCCGTTTGATTGGATGGAGTTGATCTCGCTTCAGG
GTAAAACGAATTTCTTCGAGAAGAGGGTTGGTGATTACCAGAAGGCTTCCGTCATGTCTAGCGTTAACGGAAACGGCGCG
TTTGATAACCATGTGTTCTCGCTAGACGAGGATTTTTAG

Alignment

ORF - retro_brap_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.87 %
• Parental protein coverage: 94.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SEEPLLTAQNQRFTMFPIRYKSIWEMYKKAEASFWTAEEVDLSTDVQHWE-KLSDSEKHFISHVLAFFAA
          .EEPLLT....RF.MFPI.Y..IWEMYKKAEASFWTAEEVDLS.D...WE..L.D.E.HFI.HVLAFFAA
Retrocopy AEEPLLTPTPDRFCMFPIHYPQIWEMYKKAEASFWTAEEVDLSQDTRDWETNLNDGERHFIKHVLAFFAA

Parental  SDGIVLENLAARFLNDVQVPEARAFYGFQIAMENIHSEMYSQLLETFIKDSQEKDRLFNAIETIPCISNK
          SDGIVLENLA.RF..DVQV.EARAFYGFQIA.ENIHSEMYS.LL.T.IKD..E.D.LF.AIETIPC...K
Retrocopy SDGIVLENLASRFMSDVQVSEARAFYGFQIAIENIHSEMYSLLLDTYIKDNKERDHLFRAIETIPCVAKK

Parental  AKWCLDWIQSPMSFAVRLVAFACVEGIFFSGSFCAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLLY
          A.W.L.WI.....FA.R.VAFACVEGIFFSGSFC.IFWLKKRGLMPGLTFSNELISRDEGLHCDFACL.Y
Retrocopy AQWALKWIDGSQTFAERIVAFACVEGIFFSGSFCSIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLIY

Parental  SLLQKQLPVEKVYQIVHEAVEIETEFVCKALSCDLIGMNSNLMSQYIQFVADRLLVTLGCERRYKADNPF
          .LL...L..E.V..IV..AVEIE.EFVC.AL.C.L.GMN..LMSQYI.FVADRLL..LG....Y...NPF
Retrocopy TLLRTKLSEERVKSIVCDAVEIEREFVCDALPCALVGMNRDLMSQYIEFVADRLLGALGYGKVYGVANPF

Parental  DWMEFISLQGKTNFFEKRVGEYQKASVMSSLQEGN--KNYEFKIDEDF
          DWME.ISLQGKTNFFEKRVG.YQKASVMSS........N..F..DEDF
Retrocopy DWMELISLQGKTNFFEKRVGDYQKASVMSSVNGNGAFDNHVFSLDEDF

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_7 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00025p00110680	1 retrocopy	retro_atri_2,
Brassica rapa	Bra014962	1 retrocopy	retro_brap_7 ,
Prunus persica	PRUPE_ppa008063mg	1 retrocopy	retro_pper_7,
Solanum lycopersicum	Solyc01g080210.2	1 retrocopy	retro_slyc_6,
Theobroma cacao	TCM_020494	1 retrocopy	retro_tcac_4,
Vitis vinifera	VIT_05s0020g02560	1 retrocopy	retro_vvin_20,