RetrogeneDB ID: retro_brap_19

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A06:10508029..10509238(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra018137
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra009397
• Aliases: None
• Description: None

Sequence

>retro_brap_19
ATGGCAGCAGCTTCTTCGATTTCAATTGGATCAACCGTTCCCAGAGCCTCCTCCTCCTCCTCCTCCTCCTCCTTACCGCA
GTCAAGGGCACAAGCTGTCAACTTCAACTACTCCCTCCCTCGTTTCACCGCTCTGAGGTCATCCACTCTCCTCTCTGGAC
CAGATTCCTCTTCTTTCGCCAAGTCTCTCCGCGGCTCCGTAACGAAACCTCAATCAACAGACACGAAGCCCTACGGATTG
AACATCAACGCTTCGTACAAAGTGTCGGTCCTCGGTGCTGCCGGAGGGATCGGCCAGCCTCTGTCCCTTCTCATCAAAAT
GTCTCCTCTCGTCTCCACCCTCCACCTCTACGATATCGCCAACGTCAAGGGAGTCGCCGCTGATCTGAGCCACTGCAACA
CTCCCTCTCAGGTCCGTGATTTCACCGGACCGGCTGAGCTGGCCGATTGTTTGAAAGATGTCAACGTCGTTGTCATCCCC
GCTGGTGTGCCGAGAAAGCCCGGTATGACCCGTGACGATCTCTTCAACATCAACGCCGGTATAGTGAAGACGCTTGTTGA
GGCTGTCGCTGGTAACTGTCCTAACGCCTTCATCCACATCATCAGCAACCCTGTTAACTCCACCGTCCCCATTGCTGCTG
AGGTGTTGAGGAAGAAAGGTGTCTATGATCCCAAGAAGCTCTTTGGCGTCACCACTTTGGATGTTGTGAGGGCGAACACC
TTTGTTTCTCAGAAAAAGAACTTGAAGCTCATCGATGTTGATGTTCCGGTCATCGGTGGCCACGCTGGAATCACCATTCT
GCCTCTTTTGTCGAAGACCAAGCCTTCGGTCAGCTTCACTGACGAAGAGATCGAGAAACTCACTGTGAGGATTCAGAACG
CTGGAACCGAGGTGGTGGATGCTAAGGCGGGTGCTGGCTCGGCTACTTTGTCGATGGCGTATGCCGCAGCGAGATTTGTG
GAGTCGTCTCTTCGTGCTCTTGACGGAGATGGAGATGTTTACGAGTGCTCTTTCGTGGACTCTACTCTCACTGATCTTCC
TTTCTTTGCATCACGGATCAAGATTGGGAGGAACGGAGTTGAAGCTGTGATTGAGTCTGACCTCCAAGGGCTGACTGAGT
ATGAGCACAAGGCGTTAGAAGCTCTTAAGCCTGAACTGAAAGCTAGCATCGAAAAGGGTGTTGCATTCGCAAACAAACCT
GCTAACTAA

Alignment

ORF - retro_brap_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.19 %
• Parental protein coverage: 87.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AGFKVAILGAAGGIGQSLSLLMKMNPLVSLLHLYDVVNAPGVTADVSHMDTGAVVRGFLGAKQLADALTG
          A..KV..LGAAGGIGQ.LSLL.KM.PLVS.LHLYD..N..GV.AD.SH..T...VR.F.G...LAD.L..
Retrocopy ASYKVSVLGAAGGIGQPLSLLIKMSPLVSTLHLYDIANVKGVAADLSHCNTPSQVRDFTGPAELADCLKD

Parental  MDLVIIPAGVPRKPGMTRDDLFKINAGIVKTLCEGVAKCCPNAIVNLISNPVNSTVAIAAEVFKKAGTYD
          ...V.IPAGVPRKPGMTRDDLF.INAGIVKTL.E.VA..CPNA....ISNPVNSTV.IAAEV..K.G.YD
Retrocopy VNVVVIPAGVPRKPGMTRDDLFNINAGIVKTLVEAVAGNCPNAFIHIISNPVNSTVPIAAEVLRKKGVYD

Parental  PKKLLGVTTLDVARANTFVAEVLGLDPREVDVPVVGGHAGVTILPLLSQVKPPSSFTPSETEYLTNRIQN
          PKKL.GVTTLDV.RANTFV.....L....VDVPV.GGHAG.TILPLLS..KP..SFT..E.E.LT.RIQN
Retrocopy PKKLFGVTTLDVVRANTFVSQKKNLKLIDVDVPVIGGHAGITILPLLSKTKPSVSFTDEEIEKLTVRIQN

Parental  GGTEVVEAKAGAGSATLSMAYAAAKFADACLRGLRGDANVVECSFVASQVTELPFFATKVRLGRTGAEEV
          .GTEVV.AKAGAGSATLSMAYAAA.F....LR.L.GD..V.ECSFV.S..T.LPFFA.....GR.G.E.V
Retrocopy AGTEVVDAKAGAGSATLSMAYAAARFVESSLRALDGDGDVYECSFVDSTLTDLPFFASRIKIGRNGVEAV

Parental  YQ--LGPLNEYERVGLEKAKEELAGSIQKGVDFIRK
          ....L..L.EYE...LE..K.EL..SI.KGV.F..K
Retrocopy IESDLQGLTEYEHKALEALKPELKASIEKGVAFANK

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_19 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	AT5G09660	1 retrocopy	retro_atha_10,
Brassica rapa	Bra009397	1 retrocopy	retro_brap_19 ,
Brachypodium distachyon	BRADI4G00910	1 retrocopy	retro_bdis_5,
Triticum aestivum	Traes_5AL_31CDB68F2	1 retrocopy	retro_taes_27,