RetrogeneDB ID: retro_brap_4

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A07:4085274..4086759(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra015034
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra036718
• Aliases: None
• Description: None

Sequence

>retro_brap_4
ATGGCAGAACAGAGATCAAGATCAACAAAAACCTTCTTCTCTCATCAGATGATTCTATGTCTCTTTCTTGTCTCACAAGT
CTCCATCGCCTCTTGTAGCAATACGAGTGTAGGAGTGAACTGGGGAACAATGGCGAGTCACCAGCTTCCACCTGAAAACG
TGGTGAAGATGCTAAAGGACAATGGATTTACTAAGCTAAAACTGTTCGAAGCCGACCAAAACATCTTAAACGCTCTAACT
GGTTCAGACATCGAAGTCATGATCGGAATACCAAACCGGTTGCTTAAAGAAGTCGCTCAAGATCCAGCGTTAGCAGCTTC
ATGGGTAGAAGAGAACGTCACCGCTTATTCTTACAACGGTGGAGTCAACATCAAGTACATAGCTGTCGGAAACGAGCCTT
TCCTTCAGACATATAACGGAACATACGTTGAGTTCACTTTACCAGCTCTCGTCAACATACAAAAAGCACTAGAGGAAGCT
GGTCTGAAAAACGTGAGAGTCACGGTTCCTTTCAACGCAGACATCTACTTTTCTCCTGAATCAAACCCTGTCCCATCAGC
TGGAGACTTTAGGCCTGAGCTCAGAGATGTAACGATTGAGATAATCAACTTCTTGTATACACATGATTCTCCTTTCACGG
TCAACATCTACCCTTTTCTAAGTCTTTACGGAAACGCTTACTTCCCCGTGGATTTCGCCTTCTTTGATGGGAGTAACAAC
TCTTTGAGAGATGGAGATTTGGTTTATAATAATGTGTTTGATGCGAATCTCGACACTTTGGTTTGTGCAATGGAAAGATA
CAGCTTCTTGGGGATGAAGATCATCGTGGGAGAAGTTGGATGGCCTACGGACGGAGACAAGAACGCTAACGCGAAGAGTG
CAAAGAGATTCAACCAGGGAATGGTAAAGCATGCTATGTCTGGTAATGGAACTCCAGCGAGGAAAGGAGTGATCATGGAT
GTTTATCTCTTCAGCCTTGTCGATGAAGATGCTAAGAGTATTGCTCCGGGGACTTTTGAGAGGCATTGGGGCATCTTCGA
GTTTGATGGTAGACCCAAATACGAGCTTGATTTGTCTGGTAAAGGTGATGATAAGACTCTGGTTCCTGTACAAGATGTGA
AGTATCTTCCTAAAACGTGGTGTGTTCTCGACACTAACGCGTTTAACCTCGATGACTTGGCTGATAACGTCGACTACGCT
TGTAGCTTATCTGATTGTACAGCGCTTGGGTATGGTTCCTCTTGCAACCATCTTACAAACGTGGGCAATGCTTCGTATGC
TTTTAATATGTATTATCAGATGCATGATCAGAAAACATGGGACTGTGATTTCTTGGGGTTGGGTTTGATCACTGATGAAG
ATCCCTCTGATGATCTTTGTGAGTTCCCTGTGATGATTGATACAGGCAACTCACCGAGGTTGCAGCCTCTATCTTCTAGA
GTGTTGGCCATGGTTATAGTTATTTTGGTTCTTCCCCTTTTGTAA

Alignment

ORF - retro_brap_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.07 %
• Parental protein coverage: 94.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LGVNWGTMATHKLPPKTVVQMLKDNNINKVKLFDADETTMGALAGSGLEVMVAIPNDQLKVMGSYDR-AK
          .GVNWGTMA.H.LPP..VV.MLKDN...K.KLF.AD.....AL.GS..EVM..IPN..LK........A.
Retrocopy VGVNWGTMASHQLPPENVVKMLKDNGFTKLKLFEADQNILNALTGSDIEVMIGIPNRLLKEVAQDPALAA

Parental  DWVRKNVTRYNFNGGVNITFVAVGNEPFLKSYNGTFINLTFPALQNIQNALNEAGLGNSIKATVPLNADV
          .WV..NVT.Y..NGGVNI...AVGNEPFL..YNGT....T.PAL.NIQ.AL.EAGL.N....TVP.NAD.
Retrocopy SWVEENVTAYSYNGGVNIKYIAVGNEPFLQTYNGTYVEFTLPALVNIQKALEEAGLKN-VRVTVPFNADI

Parental  YDSPVSDPVPSAGRFRPDILGQMTQIVDFLGKNNAPITINIYPFLSLYGNDDFPINYAFFDGAQ-PIDDH
          Y.SP.S.PVPSAG.FRP........I..FL.....P.T.NIYPFLSLYGN..FP...AFFDG......D.
Retrocopy YFSPESNPVPSAGDFRPELRDVTIEIINFLYTHDSPFTVNIYPFLSLYGNAYFPVDFAFFDGSNNSLRDG

Parental  GVSYTNVFDANFDTLVSSLKAVGHGDMPIIVGEVGWPTEGDKHANNGEAYRFYNGLLPRLGTNKGTPLRP
          ...Y.NVFDAN.DTLV..........M.IIVGEVGWPT.GDK.AN...A.RF..G.........GTP.R.
Retrocopy DLVYNNVFDANLDTLVCAMERYSFLGMKIIVGEVGWPTDGDKNANAKSAKRFNQGMVKHAMSGNGTPARK

Parental  TYI-EVYLFGLLDEDAKSIAPGAFERHWGLFRFDGQPKFPLDLSGQGQNKLLIGARNVTYLPNKWCMFNP
          ..I..VYLF.L.DEDAKSIAPG.FERHWG.F.FDG.PK..LDLSG.G..K.L.....V.YLP..WC....
Retrocopy GVIMDVYLFSLVDEDAKSIAPGTFERHWGIFEFDGRPKYELDLSGKGDDKTLVPVQDVKYLPKTWCVLDT

Parental  NAKDLTKLAQNIDFACTFSDCTALGYGSSCNGLDANGNASYAFNMYFQVKNQDEEACIFQGLATVTTQNI
          NA..L..LA.N.D.AC..SDCTALGYGSSCN.L...GNASYAFNMY.Q...Q....C.F.GL...T....
Retrocopy NAFNLDDLADNVDYACSLSDCTALGYGSSCNHLTNVGNASYAFNMYYQMHDQKTWDCDFLGLGLITDEDP

Parental  SQGQCDFPVQIVASSSSYVSFSLVWLVAEVLLVLM
          S...C.FPV.I....S...........A.V...L.
Retrocopy SDDLCEFPVMIDTGNSPRLQPLSSRVLAMVIVILV

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_4 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 rapa	Bra036718	1 retrocopy	retro_brap_4 ,
Arabidopsis lyrata	scaffold_200850.1	1 retrocopy	retro_alyr_28,