RetrogeneDB ID: retro_brap_21

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A08:20335405..20336764(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra030796
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra014819
• Aliases: None
• Description: None

Sequence

>retro_brap_21
ATGGCCTCCTCATCTCTCCATTTCTTCTTCTTAGCCCTTCTCTTGCCGCTCACGCTTACCACCGCCACACGTGACACATG
CGCTACCGCCGCTCCCGATGGTTCCGACGATCTCTCAATCATTCCCGTTAACGCAAGATGCTCACCCTTCGCAGCAAATC
CTACCTCCACATCCGTCATGGACACCGTCCTCCACATGGCCTCCGCAGACTCTCACCGCCTCGCATACCTCTCGAGCCTC
GTCGCCGACAAACCCAACCGAACCTCCGTCCCCGTCGCCTCCGCCAACCAGCTCCTCCACACGGGCAACTACGTCGTCCG
AGCCAGACTCGGCACCCCTCCTCAGCTCATGTTCATGGTCCTAGACACCAGCAACGACGCTGTCTGGCTCCCTTGCTCCG
GCTGCTCGGGCTGTTCCACCGCCGCGACCGCCGCTTACTTCAATCCTAACTCCTCCTCCACATACTCCACCGTCTCTTGC
TCCGCCGCGCAATGCACGCAAGCACGTGGCCTCACGTGCCCATCCTCCTCGCCTTCACCACCGTCGTCAGTCTGCTCCTT
CAACCAATCCTACGGCGGAGGCTCGTCCTTCTCCGCCTCGCTCGTCCAAGACACGCTGACGTTAGCCTCCGACGTCATCT
CCAACTTCTCCTTCGGATGCATCAACTCCGCCTCAGGGAACTCTCTACCACCGCAAGGGCTAATGGGCCTTGGACGCGGG
CCCACTTCTTTAATCTCTCAAACGACGTCGCTTTACTCAGGCGTGTTCTCCTACTGCCTCCCTAGCTTCAGGTCCTTCTA
CTTCTCCGGGTCGTTGAAACTGGGCCCAATGGGCCAACCGAGATCCATCAGATACACCCCACTCCTCCGCAGCGCTCACC
GTCCTTCGCTTTACTACGTCAATCTCACAGGAGTGAGTGTGGGACCCACACAGGTTCCCGTTGACCCAACGTACTTGACG
TTTGACTCAAGTTCAGGCGCCGGTACGATAATCGATTCCGGTACAGTAATCACCCGGTTTGTCCAACCGGTTTACGAGGC
CATCAGAGACGAGTTTAGGAGCCAGGTGAAAGGGCCGTTCTCGACGCTGGGAGCGTTCGACACGTGTTTCGCGGCGGATA
GCGATAACTTGGCGCCAAAGGTAACGCTGCACATGACGTCACTCGATTTGAAGCTGCCGGTGGAGAACACGCTTATACAC
AGCAGCGCGGGAACGCTGGCGTGTCTGTCGATGGCGGGGATACCGTTGAACGCGAACGCTGTTCTGAACGTGATCGCGAA
TCTGCAGCAGCAGAATCTGAGGATCTTGTTTGATGTTGCTAATTCTCGCCTAGGCATTGCTACTGAGGCATGCAACTAA

Alignment

ORF - retro_brap_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.28 %
• Parental protein coverage: 70.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSVLFDPSKSNSSRTLPCEAPQCKQAPNPTCTVSKSCGFNMTYGG-SAITASLTQDTLTLASDVIPNYTF
          S.V..........R.L.C........P.P...V...C.FN..YGG.S...ASL.QDTLTLASDVI.N..F
Retrocopy STVSCSAAQCTQARGLTCPS----SSPSPPSSV---CSFNQSYGGGSSFSASLVQDTLTLASDVISNFSF

Parental  GCINQATGTSLPAQGLMGLGRGPLSLISQTQNLYMSTFSYCLPNSKSSNFSGSLRLGPKFQPLRIKTTPL
          GCIN.A.G.SLP.QGLMGLGRGP.SLISQT..LY...FSYCLP...S..FSGSL.LGP..QP..I..TPL
Retrocopy GCINSASGNSLPPQGLMGLGRGPTSLISQTTSLYSGVFSYCLPSFRSFYFSGSLKLGPMGQPRSIRYTPL

Parental  LKNPRRSSLYYVNLVGIRVGNKIVDIPTSALAFDPATGAGTIFDSGTVFTRLVEPAYLAVRDEFRRRVKN
          L....R.SLYYVNL.G..VG...V......L.FD...GAGTI.DSGTV.TR.V.P.Y.A.RDEFR..VK.
Retrocopy LRSAHRPSLYYVNLTGVSVGPTQVPVDPTYLTFDSSSGAGTIIDSGTVITRFVQPVYEAIRDEFRSQVKG

Parental  ANATSLGGFDTCYSGSV--VFPPVTFMFAGMNVTIPPDNLLIHSSSGNTSCLAMAAAPNNVNSVLNVIAS
          ...T.LG.FDTC.........P.VT..........P..N.LIHSS.G...CL.MA..P.N.N.VLNVIA.
Retrocopy PFST-LGAFDTCFAADSDNLAPKVTLHMTSLDLKLPVENTLIHSSAGTLACLSMAGIPLNANAVLNVIAN

Parental  MQQQNHRVLIDVPNSRLGISRETC
          .QQQN.R.L.DV.NSRLGI..E.C
Retrocopy LQQQNLRILFDVANSRLGIATEAC

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_21 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica rapa	Bra014819	1 retrocopy	retro_brap_21 ,
Medicago truncatula	MTR_8g039540	1 retrocopy	retro_mtru_20,
Populus trichocarpa	POPTR_0001s06560	1 retrocopy	retro_ptri_13,
Prunus persica	PRUPE_ppa005966mg	1 retrocopy	retro_pper_11,
Theobroma cacao	TCM_045111	1 retrocopy	retro_tcac_5,
Vitis vinifera	VIT_13s0084g00820	1 retrocopy	retro_vvin_28,