RetrogeneDB ID: retro_brap_23

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A06:5868349..5869804(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra026149
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra031522
• Aliases: None
• Description: None

Sequence

>retro_brap_23
ATGGCAGAACTTGAAGATTCTTTCCTCGCAGAGATCGACGAGTTATCCGACTATGAAGAATCAGGATTCGAAGACAACGT
CCCAAACTATGGAGAAGATATCTCCATGGACATGTCAGACTTGGAAACCCTAAAGTCTGACGATGACCTCGACACCGTCT
CTAAGCTACTGAGAACTCAAAGATACGCTGACGTAATGAACAAGGTGGAAGACGCTCTCGGCAAGGATTCGTGTGGAGCT
TTGTCAGAAGACGATCCTCTATACAAACTAATCGTGGACTGCAACAAGCTCACAGTAGATATCGAGAACGAGATCGTCAC
CGTCCACGGCTTTATCCGTTCCAAATACAGACCTAGGTTTCCAGAGCTGGAGTCGCTTGTGCATCACGCAATCGAGTACG
CTAGCGTCGTGAAACAGATCGGGGACGAGAAGGACTTAACCCTAGTTACTCTCAAAGGTCTCTCGGCAAAAAGTACTCCC
TTATCTGTTTTACTCTTTGCTTCGACCACTAAAGGGAAGCCTCTCCCAGAAGGTGTCTTGCAAAAGACGTTAGAGGCGTG
TGATCGAGCTTTTGAGCTTGACTCCGCGCTGAAGAAGATTCTTGCCTTCGTTGAAACCAAGATGGGATGTATAGCACCGA
ATCTCTCAGCCGTTGTGGGGAGTAAAGTTGCAGCTAAGCTCATGGCTACGGCTGGAGGCTTGTCAGGGCTTGCTAAGATG
CCTTCTTGTAACGTTCAAGTTCTTGGTCAGAAGAGGAAGAATCTTGATGGATTCTCTGCTGTAACCACACAGTCTCGTGT
GGGTTACCTGGAGCAGACTGAGATTTTTCAAAACACTCCTCCTGGATTTAAGAAGCAAGCTATCAAACTCTTGGCTGGGA
AGTCTACTCTGGCAGCTAGGGTTGACGCTTGTAGGGGAGACCCGTTGGGGACTAATGGTAAAGCTCTGAGGGAAGAGATT
CAGAAGAAGATTGACAAGTTGCAAGAGCCTGGTGTTGCAAGGCAGCCTAAGCCACTTCCTGTTCCAGATATGACTGCTAA
GAAGAAGAGAGGTGGTCGGCGGCTAAGGAAAATGAAGGAAAGGTACGCGGTGACGGAGATGAGGAAGCTTTCCAACAGGG
TGGCGTTTGGTGTAGCGTCTGAAGAGAGCTCGCTTGGGGATGGGTTAGGTGTAGGGTATGGGATGCTTGGTCAGGGTGGG
AGCAAGAGGCTGAGAGTTTCCAGCGTTCCGAGTAAGCTGAAACTTGGTGCTAAGCTGGAGAAGAAGCTTAAAGAAAGACA
GTATACGAGTGGTGTTACTACTGCAACCACTTCTGGTTTCATGACATCAAGACTTGCTTTCACACCTGTGCAGGGAATAG
AGCTGTGCAATCCTGGAGCTGTGAAATTAGGTAGTGGGACTCAGAGCACTTACTTCTCTGAGTCAGGAACCTTCTCCCAG
ATCAAGAAGATATAA

Alignment

ORF - retro_brap_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.93 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATLEDSFLADLDDLSDNEAELDESDGDDAKKDEEDIDMDMADLETL-NYDDLDSVSKLQKSQRYLDIMQ
          MA.LEDSFLA..D.LSD.E........D......EDI.MDM.DLETL...DDLD.VSKL...QRY.D.M.
Retrocopy MAELEDSFLAEIDELSDYE---ESGFEDNVPNYGEDISMDMSDLETLKSDDDLDTVSKLLRTQRYADVMN

Parental  KVEEALGKESDGTEKGTVLEDDPEYKLIVDCNQLSVDIENEIAIVHNFIRDKYRLKFQELESLVNHPIDY
          KVE.ALGK.S.G.......EDDP.YKLIVDCN.L.VDIENEI..VH.FIR.KYR..F.ELESLV.H.I.Y
Retrocopy KVEDALGKDSCG----ALSEDDPLYKLIVDCNKLTVDIENEIVTVHGFIRSKYRPRFPELESLVHHAIEY

Parental  ARVVKKIGNETDLTLVDLEGLLPSAIIMVVSVTALTTKGSPLPEDVLQKTLEACDRALDLDSARKKVLDF
          A.VVK.IG.E.DLTLV.L.GL........V...A.TTKG.PLPE.VLQKTLEACDRA..LDSA.KK.L.F
Retrocopy ASVVKQIGDEKDLTLVTLKGLSAKSTPLSVLLFASTTKGKPLPEGVLQKTLEACDRAFELDSALKKILAF

Parental  VESKMGSIAPNLSAIVGSAVAAKLMGTAGGLSALAKMPACNVQVLGHKRKNLAGFSSATSQLRVGYLEQT
          VE.KMG.IAPNLSA.VGS.VAAKLM.TAGGLS.LAKMP.CNVQVLG.KRKNL.GFS..T.Q.RVGYLEQT
Retrocopy VETKMGCIAPNLSAVVGSKVAAKLMATAGGLSGLAKMPSCNVQVLGQKRKNLDGFSAVTTQSRVGYLEQT

Parental  EIFQSTPPALKSRAGRILAAKSTLAARVDATRGDPSGTNGKALREEIRKKIEKWQEPPPARQPKPLPVPD
          EIFQ.TPP..K..A...LA.KSTLAARVDA.RGDP.GTNGKALREEI.KKI.K.QEP..ARQPKPLPVPD
Retrocopy EIFQNTPPGFKKQAIKLLAGKSTLAARVDACRGDPLGTNGKALREEIQKKIDKLQEPGVARQPKPLPVPD

Parental  SEPKKRRGGRRLRKMKERYAVTDMRKLANRMAFG-TPEESSLGDGLGEGYGMLGQAGSNRLRISSVPSKL
          ...KK.RGGRRLRKMKERYAVT.MRKL.NR.AFG...EESSLGDGLG.GYGMLGQ.GS.RLR.SSVPSKL
Retrocopy MTAKKKRGGRRLRKMKERYAVTEMRKLSNRVAFGVASEESSLGDGLGVGYGMLGQGGSKRLRVSSVPSKL

Parental  KINPTIAKKLKERNYAGG---ATTSG-LTSSLAFTPVQGIELCNPQQALGLGSGTQSTYFSESGTFSKLK
          K......KKLKER.Y..G...ATTSG..TS.LAFTPVQGIELCNP..A..LGSGTQSTYFSESGTFS..K
Retrocopy KLGAKLEKKLKERQYTSGVTTATTSGFMTSRLAFTPVQGIELCNP-GAVKLGSGTQSTYFSESGTFSQIK

Parental  KI
          KI
Retrocopy KI

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_23 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	AT1G60170	1 retrocopy	retro_atha_27,
Brassica oleracea	Bo1g091740	1 retrocopy	retro_bole_6,
Brassica rapa	Bra031522	1 retrocopy	retro_brap_23 ,
Solanum tuberosum	PGSC0003DMG400004771	1 retrocopy	retro_stub_45,