RetrogeneDB ID: retro_brap_25

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A03:8443329..8444451(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra023058
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra007114
• Aliases: None
• Description: None

Sequence

>retro_brap_25
ATGTGGTTACCTAAACTCGACTACAGTAGTAGAAAGTATTTAGAGTCCGGACGCGCGAAGTTACGGCGTTTTCTTAACAA
GAATCTGCCATTACACAGAGCTCCGATTATAGAAAGCTTCCGCCTCGATTTTATTGCTTCACAATTCAAACCCGTGACAA
TTAGATCATGGCTTCTAACCGCAGTTTCACGCAACCTACGAGAGGTGGAGGTTTCTCATGGTTGTAATAATAAGGTGCTC
AACATGTTGCCAAGTAGCTTGTATACTTGTAAATCACTCGTGTCCGTGAAACTCAATGGAAGAAGGCTTCTAGTGGATGT
TCCTCGTATGGTTTCTCTCCCTTGTCTGAAAACTTTGCTGCTTCAGGATGTTGAGTACAAGAATGAAGATTCTCTTCAGC
GGCTTCTATCTAATTGCCCTGTTCTTGAAGATCTAGTGGTGGAAGGATGCAAAGGTGACAATATGGTAAAGTTCATTGTT
ATCGTCCCCTCGTTGCAACGTTTAACAGTCAATATACTTGAGGATCTAGATGAGTTTGTGATGGATACTCCTTCTTTGAA
ATACTTCAAACTTGACTACTATAATTACAAGAATCACCACTGTTTGATTGAGCGTATGCCTAAGCTGGAGGAGGCATATG
TAGAACTTAGCTTTAATCATGTTTATATTGATAGGTTTATCGGATCAATCACTTTTGTCAAACGTCTGACGTTATGCATA
GATGATGTGTATGGTGATGGTTTTGTCTTCGACCAGCTTGAACATCTGCAACTATGCACATGCGATGAACAACATACGTC
GGGTGCGGTGATTGTCCGGTTGCTCAAAGATTCACCTAACTTACGAGTACTAGACCTATTCAAAATGGAATACCATAACC
CTATTGGTCTGTATACTTGGAATCAACCAAGTACTGTTCCGGAATGTATTTTGTCGAGTCTACAAACTTTCAAGTGTTCA
GGATACTTAGGAAGACCACGAGAAAGAGATCTTGTGATTTATATATTAAAAAATGCTAATAACTTAAAGACTGCAACAAT
CTGGTTTCCGACGGTTGACATGAAAAAAGAGTTGGTTCTTTCTTCTCGAGCTTCAAACGCATGCCAACTTGTATTTGATT
GA

Alignment

ORF - retro_brap_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.85 %
• Parental protein coverage: 83.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MWLPKLKYGHMYCSESEWEKLQCFLDRNLPLHRAPVIESFRLELFNTRLKPENIKMWLVLALSHSLRELE
          MWLPKL.Y......ES...KL..FL..NLPLHRAP.IESFRL.......KP..I..WL..A.S..LRE.E
Retrocopy MWLPKLDYSSRKYLESGRAKLRRFLNKNLPLHRAPIIESFRLDFIASQFKPVTIRSWLLTAVSRNLREVE

Parental  IVYVSYPNRLNILPSNLFTCKSLVILKLGG-RILLDVTRLVSLPSLKTLRLLKVKYFKDETLQRLLSNCP
          .........LN.LPS.L.TCKSLV..KL.G.R.L.DV.R.VSLP.LKTL.L..V.Y.....LQRLLSNCP
Retrocopy VSHGCNNKVLNMLPSSLYTCKSLVSVKLNGRRLLVDVPRMVSLPCLKTLLLQDVEYKNEDSLQRLLSNCP

Parental  ILEDLMVDLHERDTTTTKFTALVPSLQRLTLRIPDNPHIDGFMIETPALKYFKLSGNIRNYHYCSIENMP
          .LEDL.V.....D....KF...VPSLQRLT..I......D.F...TP.LKYFKL.......H.C.IE.MP
Retrocopy VLEDLVVEGCKGD-NMVKFIVIVPSLQRLTVNILED--LDEFVMDTPSLKYFKLDYYNYKNHHCLIERMP

Parental  NLIEAHLDVEFPD--IKSLIGSATSVKRLTLCSKTLLAEGFVFNQLEHLEVCTCPMIFSNQLV--RLLKA
          .L.EA.....F....I...IGS.T.VKRLTLC.......GFVF.QLEHL..CTC........V..RLLK.
Retrocopy KLEEAYVELSFNHVYIDRFIGSITFVKRLTLCIDDVYGDGFVFDQLEHLQLCTCDEQHTSGAVIVRLLKD

Parental  SPKLKRLDISVVNHHKPIGMDEWNQPSTVPECLLSSLQTLSWSGEYIGEPQERDIVVYILKHALHLKTAT
          SP.L..LD......H.PIG...WNQPSTVPEC.LSSLQT...SG.Y.G.P.ERD.V.YILK.A..LKTAT
Retrocopy SPNLRVLDLFKMEYHNPIGLYTWNQPSTVPECILSSLQTFKCSG-YLGRPRERDLVIYILKNANNLKTAT

Parental  I
          I
Retrocopy I

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_25 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	Bra007114	1 retrocopy	retro_brap_25 ,