RetrogeneDB ID: retro_brap_5

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A07:13510257..13511667(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra003505
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra005441
• Aliases: None
• Description: None

Sequence

>retro_brap_5
ATGAGAAGAGGAGGGTTTCGTGTGTTGGATATGGTGAAACCGTTTTTGCCGTATCTGCCAGAAGTGCAGAGTGCTTTTGA
GAAGAAGAAGAAGGTTCCATTGAGAGAGAAGGTCATCTATACCCTGACCACTCTCTTCGTGTTTCTCGTTTGTAGTCAAC
TTCCTCTCTACGGTATCCACTCCACCACCGGCGCGGATCCATTCTACTGGATGCGTGCCATCCTCGCCTCGAGCCGTGGC
ACCCTCATGGAGCTCGGTATCGGTCCCATCATCACATCAGGGCTCGTGATGCAGTTCTTGACTGGCTCAAAGATTATTCA
GGTCAACGATGAGGAGGATCATGCTCTCTTGAACGCTGCTCAGAAGCTTCTCGGCGTTCTGATCGCCTTAGGTCAAGCCG
TGACATACGTCCTCTCTGGTATGTACGGTCCAGTCGCACAGCTCGGCGTGGGAAACGCACTTCTCATCGTTCTCCAGCTT
GTCTTTGCCGGAGTCATCCTTCAGTGTCTGGACGAGCTTCTCCAAAAGGGGTATGGTCTTGGCTCAGCGATCTCCCTTTT
CATAGCGACTAGCCTCTGCGAGAGCGTTATATGGAAAGCCTTTAGCCCCGTTACGTTCAACAACATCGGACGGTCTGGAC
AGGAGTTTGAAGGCGCGTTGATCTCGCTCTTCCATAACCTCATAACCAAGTCAAGCATCCGACAAGCTTTCTTCAGACAG
AGCCTTCCAAACGTTACAAACTTGCTTGCAACAGTCTTGGTCTTCCTCATTGTCGTCTACCTCCAAGGCTTCCGCGTTGT
GTTACCTCTTTGGTCAAAGAACTCTCGACAAGGCGGCGGCTACCCGATCAAGCTCTTGTACACCTCCAACATGCCCATCA
TTCTCCAATCCGCTCTAGTCTCAAATCTCTACTTCATCTCTCAGCTTCTCTACAACAACTTCAGCGGAAGTTTCCTGGTG
AACTTGCTGGGACAGTGGAGAGGACCCACACCAGTCGGTGGTCTCGCTTACTTGATCACAGCTCCATCAAGCCTGGCTGC
TCATCCTTGCCACACACTCTTCTACATCGTCTTCATGCTCTCTACTTGTGCCTTTCTATCAAAGACATGGATTGAAGTCT
CGGGTTCCTCCGCCAGAGACGTGGCCAAGCAGCTCAAGAAACAAGGGATGTGGATGGATGGGCACAGAGACTCCAATCTA
CACAAGGAGCTTAACCGCTACATCCCAACAACAGCCGCCTTTGGAGGAATGTGCATTGGTGCACTCACTGTTCTTGCTGA
CCTCACCGGAGCTATTGGCTCAGGGACTGGTATCTTGCTTGCCGTCACAACCATATATCAGTTTCTCGACACTTTTGACA
AGGAACTAGCCACCGAGTCACGAAGCCTTTGCCACTACACTATATTGTAA

Alignment

ORF - retro_brap_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.04 %
• Parental protein coverage: 68.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGFRVLHLVRPFLAFLPEVQSA---DRKVPFREKVIYTVISLFIFLVCSQLPLYGIHSTTGADPFYWMRV
          GGFRVL..V.PFL..LPEVQSA.....KVP.REKVIYT...LF.FLVCSQLPLYGIHSTTGADPFYWMR.
Retrocopy GGFRVLDMVKPFLPYLPEVQSAFEKKKKVPLREKVIYTLTTLFVFLVCSQLPLYGIHSTTGADPFYWMRA

Parental  ILASNRGTVMELGITPIVTSGLVMQLLAGSKIIEVDNNVREDRALLNGAQKLLGILIAIGEAVAYVLSGM
          ILAS.RGT.MELGI.PI.TSGLVMQ.L.GSKII.V..N..ED.ALLN.AQKLLG.LIA.G.AV.YVLSGM
Retrocopy ILASSRGTLMELGIGPIITSGLVMQFLTGSKIIQV--NDEEDHALLNAAQKLLGVLIALGQAVTYVLSGM

Parental  YGPVGQLGVGNAILIILQLFFAGIIVICLDELLQKGYGLGSGISLFIATNICESIIWKAFSPTTINT-GR
          YGPV.QLGVGNA.LI.LQL.FAG.I..CLDELLQKGYGLGS.ISLFIAT..CES.IWKAFSP.T.N..GR
Retrocopy YGPVAQLGVGNALLIVLQLVFAGVILQCLDELLQKGYGLGSAISLFIATSLCESVIWKAFSPVTFNNIGR

Parental  -GAEFEGAVIALFHMLITKSNKVAALRQAFYRQNLPNVTNLLATVLIFLIVIYFQGFRVVLPVRSKNARG
          .G.EFEGA.I.LFH.LITKS......RQAF.RQ.LPNVTNLLATVL.FLIV.Y.QGFRVVLP..SKN.R.
Retrocopy SGQEFEGALISLFHNLITKS----SIRQAFFRQSLPNVTNLLATVLVFLIVVYLQGFRVVLPLWSKNSR-

Parental  QQGSYPIKLFYTSNMPIILQSALVSNLYFISQLLYRKFSGNFFVNLLGQWK
          Q.G.YPIKL.YTSNMPIILQSALVSNLYFISQLLY..FSG.F.VNLLGQW.
Retrocopy QGGGYPIKLLYTSNMPIILQSALVSNLYFISQLLYNNFSGSFLVNLLGQWR

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_5 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 oleracea	Bo4g040080	1 retrocopy	retro_bole_27,
Brassica rapa	Bra005441	1 retrocopy	retro_brap_5 ,