RetrogeneDB ID: retro_brap_45

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A04:9926596..9927835(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra022833
• Aliases: None
• Description: None

Sequence

>retro_brap_45
GGTGGGCTGCTGGAAAATGAAGCTAGAGTTTCTCCTCCTCCTCCTCCCTTGAGTGGAACTAATAATAATAAAGGAGGTCG
ACCTACTTTTAAAGACTTTGGTGGGATTAAAAAAGTGTTGGATCAGTTAGAGTTTGATATTCTCTTCCCTCTTTTCAATC
CTCTAGCGTTTGAGACGACTGGAGTTAAGCCGCCACGCGGGTTTCTATTCCACGGACCACCTGGCTGTGGAAAGACTCGG
CTGGCCAATGCCATAGCCAACGAAGCTAGTGTTCCCTTTTACCAGATCTCAGCCACGGAAGTCGTCTCCGGTGTTCCTGG
TGATTCTGAAGAGAACATCAGAGAGCTCTTCTCTAAAGCACACAGGACCGCGCCTTCTATCATCTTTATCGATGAGATTG
ACGCCATTGGATCCAAGAGAGAGAAACAGCAAAGGGAGATGGAGAAGCGGATCGTAACACAGCTATTGACTTGTATAGAT
GGTCCTCATCAGCAGGGAGATGATGAAAATGGTGGATACGTTGTTGTCATTGGAGCTACTAATAGGCCTGACGCTCTTGA
TCCTGCTCTGAGAAGGCCCGGGCGGTTTGACCGTGAGATTGCTCTAACCGTTCCTGACGAAGACGCCAGGGCTGAGATAC
TCTCTGTTGTATCTAAAAGACTTAGACTCGAAGGCTCCTTCAACATGAAAGGAATCGCTCGCTTAACGCCCGGGTTTGTT
GGAGCTGATTTGGAAGGTTTAGCTAACATGGCTGGCAGTCTTTGCATCAAGAGAGTTATGAATTCAAGAAAATCGCAACT
GTCCGGCTGCCAGGATGATGATGGGTCTTGGCTGAGGCAGCCCTGGTCAGAAGAAGATTTGCAGATTCTCTTTGTGAGAA
TGTCTGATTTTGAGGAAGCGGTGAAGTTAGTCAAGGGATCTTTAACTCGAGAAGGTTTCTCCACCGTGCCTGATGTCACA
TGGGGTGATGTCGGTGGACTTGACCATCTACGGAGTGAACTCAACGATTACATAGTCAGCCCTATCAAAAATCCAGATAT
TTATAAAAAAATTGTGGCGAAGCTAGAGACAGGTTTCTTGCTCTATGGACCGCCGGGCTGCGGAAAGACGTTGGTTGCAA
AGGCAGTTGCGAACGAGGCAGGAGCTAATTTCATACACATCAAGGGTCCGGAACTTCTAAATAAATACGTTGGTGAAAGC
GAGCTTGCTATGCGGACCTTGTTTCAGCGCGCCCGGACA

Alignment

ORF - retro_brap_45 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.48 %
• Parental protein coverage: 55.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGYAKLNSSTKLAPPPPPPLSGKVG--PTFKDFAGIKKVLDELDQYILSPLLNPPLFGKIGAKPPSGILF
          GG...........PPP........G..PTFKDF.GIKKVLD.L...IL.PL.NP..F...G.KPP.G.LF
Retrocopy GGLLENEARVSPPPPPLSGTNNNKGGRPTFKDFGGIKKVLDQLEFDILFPLFNPLAFETTGVKPPRGFLF

Parental  HGPPGCGKTRLAHAVANEAGVPFYQISATQVLSGVSGESEENIRELFSKAYRTAPSIVFIDEIDAIGSKR
          HGPPGCGKTRLA.A.ANEA.VPFYQISAT.V.SGV.G.SEENIRELFSKA.RTAPSI.FIDEIDAIGSKR
Retrocopy HGPPGCGKTRLANAIANEASVPFYQISATEVVSGVPGDSEENIRELFSKAHRTAPSIIFIDEIDAIGSKR

Parental  ENQQRETEKRIVTQLLTCMDGPPPGDTAAAAGYVVVIGATNTPDALDPALRRGRRFGREIALTAPDEHAR
          E.QQRE.EKRIVTQLLTC.DGP.........GYVVVIGATN.PDALDPALRR..RF.REIALT.PDE.AR
Retrocopy EKQQREMEKRIVTQLLTCIDGPHQQGDDENGGYVVVIGATNRPDALDPALRRPGRFDREIALTVPDEDAR

Parental  AEILSLVAQRLRLEGSLDMKRIARLTPGFVGADLEELADMAASLCVKRIMDSRKLQLSGDSDDGDDRSWL
          AEILS.V..RLRLEGS..MK.IARLTPGFVGADLE.LA.MA.SLC.KR.M.SRK.QLSG..D..DD.SWL
Retrocopy AEILSVVSKRLRLEGSFNMKGIARLTPGFVGADLEGLANMAGSLCIKRVMNSRKSQLSGCQD--DDGSWL

Parental  SQPWSDEDLDKLFVRMSDFEEAVKLVKGSLTREGFSTVPDVTWDDVGGLDHLRTELDDYVVNPIKYADAF
          .QPWS.EDL..LFVRMSDFEEAVKLVKGSLTREGFSTVPDVTW.DVGGLDHLR.EL.DY.V.PIK..D..
Retrocopy RQPWSEEDLQILFVRMSDFEEAVKLVKGSLTREGFSTVPDVTWGDVGGLDHLRSELNDYIVSPIKNPDIY

Parental  EKFGKKLLETGFLLYGPPGCGKTLVAKAVANEAGANFIHIKGPELLNKYVGESERAIRTLFQRART
          .....K.LETGFLLYGPPGCGKTLVAKAVANEAGANFIHIKGPELLNKYVGESE.A.RTLFQRART
Retrocopy XXXVAK-LETGFLLYGPPGCGKTLVAKAVANEAGANFIHIKGPELLNKYVGESELAMRTLFQRART

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_45 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	Bra022833	1 retrocopy	retro_brap_45 ,