RetrogeneDB ID: retro_brap_57

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: Scaffold000609:1..1320(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra006013
• Aliases: None
• Description: None

Sequence

>retro_brap_57
GTAGTCCAGAGTAGAGACCCTGCCGATAAGCAAATTAATGTGACTTGTGAGGTACAACAATTATTAGGAAATAATCGAGT
TAGAGCTGTAGCTATGAGTGCTACGGACGGGTTGATGAGAGGAATGGAAGTGATTGACACGGGAGCTCCTCTCAGTGTTC
CGGTCGGTGGAGCTACTCTCGGACGAATTTTCAACGTTCTTGGGGAGCCTGTTGACAATTTGGGTCCTGTAGATAGTAGT
GCAACGTTCCCTATTCATAGATCTGCGCCTGCCTTTATCGAGTTAGATACGAAATTATCCATCTTTGAAACAGGTATTAA
GGTCGTCGATCTTTTAGCTCCTTATCGGCGTGGAGGAAAAATAGGACTATTTGGGGGGGCTGGAGTAGGTAAAACAGTAC
TGATCATGGAATTAATCAATAACATTGCTAAAGCTCATGGGGGCGTATCCGTATTCGGTGGAGTAGGGGAACGGACTCGT
GAAGGAAATGATCTTTATATGGAAATGAAGGAATCCGGAGTAATTAATGAAAAAAATATTGAGGAATCAAAGGTAGCTCT
AGTCTATGGCCAAATGAATGAACCACCGGGAGCTCGTATGAGAGTTGGTTTAACTGCCCTAACTATGGCGGAATATTTCC
GAGATGTTAATAAGCAAGATGTGCTTTTATTTATCGATAATATCTTTCGTTTTGTTCAAGCAGGATCAGAGGTATCCGCT
TTATTAGGGAGAATGCCCTCCGCAGTGGGTTATCAACCTACTCTTAGTACAGAAATGGGTTCTTTGCAAGAAAGAATTGC
TTCTACTAAAAAGGGATCTATACCTCTATTCAAGCAGTTTATGTACCTGCAGACGATTTGACCGACCCTGCCCCTGCCAC
AACATTTGCACATTTGGATGCTACTACCGTACTTTCCAGAGGATTAGCTTCCAAGGGTATTTATCCAGCAGTAGATCCTT
TAGATTCAACCTCGACTATGTTACAGCCTCGGATCGTTGGCAACGAACATTATGAAACTGCGCAAAGAGTTAAGGAAACT
TTACAACGTTACAAAGAACTTCAGGACATTATCGCAATTCTTGGCTTGGATGAATTATCGGAAGAGGATCGTTTAACTGT
AGCAAGAGCAAGAAAAATTGAGCGTTTCTTATCACAACCGTTCTTTGTGGCAGAAGTTTTTACTGGTTCTCCAGGAAAGT
ATGTTGCTCTTGCGGAAACTATTAGGGGATTTCAACTAATCCTTTCCGGAGAATTAGACGGCCTACCTGAACAGGCTTTT
TATTTGGTGGGTAACATCGATGAAGCTAGCACGAAAGCT

Alignment

ORF - retro_brap_57 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.14 %
• Parental protein coverage: 79.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IMTSLEVQDHPTRLVLEVSHHLGQNVVRTIAMDGTEGLVRGRRVLNTGAPITVPVGRATLGRIMNVLGEP
          ...S....D.......EV...LG.N.VR..AM..T.GL.RG..V..TGAP..VPVG.ATLGRI.NVLGEP
Retrocopy VVQSRDPADKQINVTCEVQQLLGNNRVRAVAMSATDGLMRGMEVIDTGAPLSVPVGGATLGRIFNVLGEP

Parental  IDERGEIKTEHYLPIHRDAPALVDLATGQEILATGIKVVDLLAPYQRGGKIGLFGGAGVGKTVLIMELIN
          .D..G........PIHR.APA...L.T...I..TGIKVVDLLAPY.RGGKIGLF...GVGKTVLIMELIN
Retrocopy VDNLGPVDSSATFPIHRSAPAFIELDTKLSIFETGIKVVDLLAPYRRGGKIGLFXXXGVGKTVLIMELIN

Parental  NVAKAHGGFSVFAGVGERTREGNDLYREMIESGVIKLGEKQSESKCALVYGQMNEPPGARARVGLTGLTV
          N.AKAHGG.SVF.GVGERTREGNDLY.EM.ESGVI.......ESK.ALVYGQMNEPPGAR.RVGLT.LT.
Retrocopy NIAKAHGGVSVFGGVGERTREGNDLYMEMKESGVINXXXIE-ESKVALVYGQMNEPPGARMRVGLTALTM

Parental  AEYFRDAEGQDVLLFIDNIFRFTQANSEVSALLGRIPSAVGYQPTLASDLGALQERITTTKKGSI-TSVQ
          AEYFRD...QDVLLFIDNIFRF.QA.SEVSALLGR.PSAVGYQPTL....G.LQERI..TKKGSI.TS.Q
Retrocopy AEYFRDVNKQDVLLFIDNIFRFVQAGSEVSALLGRMPSAVGYQPTLSTEMGSLQERIASTKKGSI<TSIQ

Parental  AIYVPADDLTDPAPATTFAHLDATTVLSRQISELGIYPAVDPLDSTSRMLSPHILGEEHYNTARGVKKVV
          A.YVPADDLTDPAPATTFAHLDATTVLSR.....GIYPAVDPLDSTS.ML.P.I.G.EHY.TA..VK...
Retrocopy AVYVPADDLTDPAPATTFAHLDATTVLSRGLASKGIYPAVDPLDSTSTMLQPRIVGNEHYETAQRVKETL

Parental  QNYKNLQDIIAILGMDELSEDDKLTVARARKIQRFLSQPFHVAEIFTGAPGKYVDLKENINSFQGLLDGK
          Q.YK.LQDIIAILG.DELSE.D.LTVARARKI.RFLSQPF.VAE.FTG.PGKYV.L.E.I..FQ..L.G.
Retrocopy QRYKELQDIIAILGLDELSEEDRLTVARARKIERFLSQPFFVAEVFTGSPGKYVALAETIRGFQLILSGE

Parental  YDDLPEQSFYMVGGIDEVVAKA
          .D.LPEQ.FY.VG.IDE...KA
Retrocopy LDGLPEQAFYLVGNIDEASTKA

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_57 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00006p00059970	1 retrocopy	retro_atri_7,
Arabidopsis thaliana	AT5G08670	1 retrocopy	retro_atha_12,
Oryza sativa indica	BGIOSGA017602	2 retrocopies	retro_oind_104, retro_oind_87,
Brassica rapa	Bra006013	2 retrocopies	retro_brap_51, retro_brap_57 ,
Chlamydomonas reinhardtii	CHLREDRAFT_78348	1 retrocopy	retro_crei_1,
Aegilops tauschii	F775_32946	1 retrocopy	retro_atau_18,
Hordeum vulgare	MLOC_70791	1 retrocopy	retro_hvul_13,
Oryza glaberrima	ORGLA01G0220100	1 retrocopy	retro_ogla_47,