RetrogeneDB ID: retro_brap_1

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A09:14856059..14857094(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra017387
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra022139
• Aliases: None
• Description: None

Sequence

>retro_brap_1
ATGAAAGGTCTCTTCAAACATAAGCCTCGTCCTCCTGGTGAAATCGTTCGTCAGACACGAGATCTCATCGCCTTGTCCGA
AAACGAAAACCAAGAAACCGACATGAAACACTCTAAACGGTTAGGAATATGTCCTGAGATCTGCAGGAACATTAGGGAAT
TGAAATCGATCCTGTACGGAAACAGCGAAGCCGAGCCTGTTGCCGAAGCGTGCCTCTCGTTGACGCAAGAGTTCTTCAGA
GAAGACACGCTTCGCCCCTTGATCAAGTCTCTTCCGAAACTCGACCTAGAGGCGAGGAAAGACGCCACGCAGATCGTAGC
GAATCTGCAGAAGCAACAAGTCGGGAGCCGACTCGTTGCTTCTGAGTATCTCGAATCAAATCTCGACGTGATCGACACGC
TAGTCGAAGGAATCGGTAGAGACCACCATTTGGCATTGCATTACACGGGGATGCTTAAAGAATGCGTTCGTCATCAGGTT
GTTGCCAAGTACATCCTCGAGTCGAAGAACCTCGAAAGATTCTTCGACTATGTCCAGCTTCCGTATTTCGATGTAGCTAC
AGACGCGAGCAAGATCTTCCGGGAGCTTTTGACCAGGCACAAGTCCACGGTATCCGAGTACCTTGCCAAGAACTATGAGT
GGTTTTTCGCGGAGTACAACACGAGGCTGTTGGAGAAAGGGAGCTACTTCACGAAGAGACAAGCTTCGAAACTCCTAGGA
GATGTGTTGATGGACCGGTCTAACTCGGGTGTGATGGTGAGGTATGTGAGCAGTTTGGATCATTTGAGGATCATGATGAA
TCTGCTGAGAGAACCGACCAAGAACATTCAGCTAGAGGCCTTCCATATCTTCAAGCTGTTTGTGGCGAACGAGAGGAAAC
CAGAGGACATTGTGGCGATTCTTGTCGCGAATCGGAACAAGATTCTTCGGTTGTTTGCTGATTTGAAGCCTGAGAAGGAA
GATGAAGGGTTTGAAGCTGATAAGTTACTGGTTGTGGGTGAGATTGCATCGCTTTCTCTCAAGCTAAGTGAATGA

Alignment

ORF - retro_brap_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.27 %
• Parental protein coverage: 98.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKGLFKSKPRTPADIVRQTRDLLLYADRSKSLPDLRESKREEKMAELSRNIRDMKSILYGNSEAEPVAEA
          MKGLFK.KPR.P..IVRQTRDL...........D...SKR.....E..RNIR..KSILYGNSEAEPVAEA
Retrocopy MKGLFKHKPRPPGEIVRQTRDLIALSENENQETDMKHSKRLGICPEICRNIRELKSILYGNSEAEPVAEA

Parental  CAQLTQEFFREDTLRLLITCLPKLNLETRKDATQLVANLQRQQVNSRLIASDYLEANLDLMDVLMEGF-E
          C..LTQEFFREDTLR.LI..LPKL.LE.RKDATQ.VANLQ.QQV.SRL.AS.YLE.NLD..D.L.EG...
Retrocopy CLSLTQEFFREDTLRPLIKSLPKLDLEARKDATQIVANLQKQQVGSRLVASEYLESNLDVIDTLVEGIGR

Parental  NTDLALHYGAMFRECIRHQIVARYVLESEHVKKFFDYIQLPNFDIAADAAATFKELLTRHKSTVAEFLIK
          ...LALHY..M..EC.RHQ.VA.Y.LES.....FFDY.QLP.FD.A.DA...F.ELLTRHKSTV.E.L.K
Retrocopy DHHLALHYTGMLKECVRHQVVAKYILESKNLERFFDYVQLPYFDVATDASKIFRELLTRHKSTVSEYLAK

Parental  NEDWFFADYNSKLLESSNYITRRQAIKLLGDILLDRSNSAVMTRYVSSRDNLRILMNLLRESSKSIQIEA
          N..WFFA.YN..LLE...Y.T.RQA.KLLGD.L.DRSNS.VM.RYVSS.D.LRI.MNLLRE..K.IQ.EA
Retrocopy NYEWFFAEYNTRLLEKGSYFTKRQASKLLGDVLMDRSNSGVMVRYVSSLDHLRIMMNLLREPTKNIQLEA

Parental  FHVFKLFAANQNKPADIINILVANKSKLLRLLADLKPDKEDERFEADKSQVLREIAAL
          FH.FKLF.AN..KP.DI..ILVAN..K.LRL.ADLKP.KEDE.FEADK..V..EIA.L
Retrocopy FHIFKLFVANERKPEDIVAILVANRNKILRLFADLKPEKEDEGFEADKLLVVGEIASL

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_1 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT5G47540	1 retrocopy	retro_atha_11,
Brassica rapa	Bra022139	1 retrocopy	retro_brap_1 ,
Populus trichocarpa	POPTR_0006s01590	1 retrocopy	retro_ptri_1,
Arabidopsis lyrata	scaffold_800035.1	1 retrocopy	retro_alyr_20,