RetrogeneDB ID: retro_brap_27

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A06:18498903..18500787(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra009992
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra005691
• Aliases: None
• Description: None

Sequence

>retro_brap_27
ATGATTACTACGATGCACTCAGAAGAATCAGGAAGAAGTAGTTACTTGCCCCGCAAGCGACATCTCGATAACCCTTCTGA
AGAACAGAGCAAAAGATCAAGACTTTACCCTCGCGATCAACACCCAAACACAAACTTCATCCCTCACGGTTGGTTAGACT
GTCCACGTTTCGGCCACGAGATCGGCCCCATCATCCCATCAAAAGTCCCACTCAGCGAATCTTACAACGACCACCTCCCT
CCCGACAAAAGATACACTTTCAAACAGCTGCTAACCAACAACAAAAGGAACAAGCTCGGTCTCGTGATTGATCTCACCAA
CACAACTCGTTACTATAACCCTAGCACAGACCTTAGAAGGGAAGGGATCGAGTACGTCAAGATTCGCTGCAGCGGTCGTG
ACTCTGTCCCTGATAACGTCTCCGTAAACACATTCGTCCACGAGGTGAATCAGTTCGAGAGACGTAACTTCTCGAAAAAG
TCTATTCTCGTTCACTGTACGCATGGACATAACCGTACAGGGTTCATGGTTGTTCATTACCTTATGAGGTCTAGTCCCTT
GATGAGCGTTACACAGGCTCTTAAAACGTTTAGCGACGCTCGTCCCCCAGGGATATATAAATCGGATTACATCGACGCTC
TCTACAGTTTCTATCACGAAACAAAGCCTGAGAGTGCTGTTTGCCCACAGACTCCTGAGTGGAAGAAGTCTGAAGAAAAC
GAGTCTTTATCTGTATCATTATCATCACCGTGTGTCCCTTTTGTGATCAAGAAGATGTCAAACGACGACGTTTTGGGAGA
TGAGATACCTTACGGTCAAGAGAAGTGTTACCAGGAGTTTTGTTACGAGATGATGAATATTAAGATAGAAGGAAGATCGT
CGTCTCTGCAGTTTCCCGGCTCGCATCCTGTGTCTTTAGACAGGGAAGGGTTCCAGCTCTTGAGGCGGAGGTACTACTAC
GCCACGTGGAAGGCGGACGGGACGCGTTACATGATGCTATTGACTAGAGAAGGATGTTATTTGATAGACAGGAAGTTTAG
ATTCAGAAGAGTGCAGATGCGGTTCCCTTGCAAGCCTCACGAGGCTAGAGTGCATGACTACACTCTGCTCGATGGAGAGA
TGGTTGTGGATAACTTCCTTGACGGGCAAGGAAAGCCTTGCCAGGCGAGGAGGTACCTCGTCTACGACATGGTAGCAGTC
AACGGGGTATCAGTATCTGACCGGCCTTTCAGTGAGAGATGGAGTGTTATCGATAGAGAAGTGATCAGACCACGTAACGA
TGAGAAGAAAGTTACAAAAGGTTACAGATACGAGATGGAGCCGTTTGGTGTACGTGTAAAAGCCTTTTGCCTACTCTCTT
CCGTGGAGAAGAAGGTGTTCAACGAGCTGATACCATCGCTCTCACACGACTCCGACGGGATCATACTCCAAGGCTGGGAC
GAGCCTTACGTCTACCAGAGGAACCAAGGCTTGCTCAAGTGGAAGTTTCTAGACACCATCGACTTTTTGTTCGAGGTGGG
GAGAGACGGGCGTTACATGCTGTTCTTGTGTGAAAACGGGAGGAACAAGCTTATGGAGGGGCACGCTGTTGAGTTTAGAG
GCGACGGTTGGGAGGAACCGGGGAGTTATAGTGGGAAGCTTTTGGAGTGTTTTTGGGATAAGGAGGATAAGGTTTGGGTG
CCTATGAGGGTTAGAGTTGATAAGTCTCAGCCGAATGGTATGGGAACTTTTCGTGGGGTGATGAAGTCTATTAATGATGG
TATAACTAAGGAGGTTTTGTTGGAGGAGATTAAAGAGATTGTTAGGCTTCCTATGTACGTTGAGCGTATTCGTATGGATA
CTCTAGCTGCGGAACGTCGCAGGCATGGGAACCGCAGGGGCTGA

Alignment

ORF - retro_brap_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.56 %
• Parental protein coverage: 54.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IVTMSNDDILGDEIPYYQEEAYRKFCYKMLMMSIGGRGCA-QFPGSHPVSLDRESLQLLRQRYYYATWKA
          I..MSNDD.LGDEIPY.QE..Y..FCY.M....I.GR....QFPGSHPVSLDRE..QLLR.RYYYATWKA
Retrocopy IKKMSNDDVLGDEIPYGQEKCYQEFCYEMMNIKIEGRSSSLQFPGSHPVSLDREGFQLLRRRYYYATWKA

Parental  DGTRYMMLLTIDGCYLIDRSFKFRRVQMRFPCRHSSGGIPDQVHHFTLLDGEMVIDNPMNEKGQ--ARRR
          DGTRYMMLLT..GCYLIDR.F.FRRVQMRFPC........D.....TLLDGEMV.DN.....G.....RR
Retrocopy DGTRYMMLLTREGCYLIDRKFRFRRVQMRFPCKPHEARVHD----YTLLDGEMVVDNFLDGQGKPCQARR

Parental  YLVYDLVAINGESVVERTFCERWNMVVHEVIKGRDVDKQRNHCYRYDLEPFGVRMKGFYLLSTVE-KLLK
          YLVYD.VA.NG.SV..R.F.ERW.....EVI..R...K.....YRY..EPFGVR.K.F.LLS.VE.K...
Retrocopy YLVYDMVAVNGVSVSDRPFSERWSVIDREVIRPRNDEKKVTKGYRYEMEPFGVRVKAFCLLSSVEKKVFN

Parental  GTIPSLSHEADGLIFQGWDDPYVPRTHKGLLKWKYAEMNSVDFLFEMGEEDEGRRMLFLFERGKKKLMDG
          ..IPSLSH..DG.I.QGWD.PYV.....GLLKWK.......DFLFE.G....GR.MLFL.E.G..KLM.G
Retrocopy ELIPSLSHDSDGIILQGWDEPYVYQRNQGLLKWKF--LDTIDFLFEVGR--DGRYMLFLCENGRNKLMEG

Parental  YTVEFR-DG-SDPSSYNGKIVECSWDKEKKVWVSMRIRVDKTTPNDINTARKVIKSINDNITEEVLLQEI
          ..VEFR.DG...P.SY.GK..EC.WDKE.KVWV.MR.RVDK..PN...T.R.V.KSIND.IT.EVLL.EI
Retrocopy HAVEFRGDGWEEPGSYSGKLLECFWDKEDKVWVPMRVRVDKSQPNGMGTFRGVMKSINDGITKEVLLEEI

Parental  REIIRLPMYADRIRMDLRAAGR
          .EI.RLPMY..RIRMD..AA.R
Retrocopy KEIVRLPMYVERIRMDTLAAER

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_27 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	Bo3g001500	1 retrocopy	retro_bole_2,
Brassica rapa	Bra005691	1 retrocopy	retro_brap_27 ,