RetrogeneDB ID: retro_brap_51

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A09:18458324..18459617(+)
• 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_51
GAAGTACAGCAATTATTAGGAAACAACCGAGTTAGAGCTGTAGCTATGAGCGCGACCGAGGGTTTAAAGAGAGGGATGGA
CGTGGTTGATATGGGAAATCCTCTAAGTGTTCCAGTCGGCGGAGCGACTCTAGGACGAATTTTCAATGTACTTGGGGAAC
CTGTTGATAATTTAGGTCCTGTCGATACTCTCACAACATCTCCTATCCATAAATCCGCGCCTGCTTTTATAGACTTAGAT
ACAACCTTATCTATTTTTGAAACAGGAATTAAAGTAGTAGATCTTTTGGCCCCTTATCGTCGTGGGGGAAAAATCGGACT
ATTCGGTGGGGCTGGCGTGGGTAAAACAGTACTAATTATGGAATTGATCAACAACATTGCCAAAGCTCATGGTGGTGTAT
CCGTATTTGGTGGAGTAGGCGAACGAACTCGTGAAGGAAATGATCTTTACATGGAAATGAAAGAATCTGGAGTCATTAAT
GAACTAAACCTTGCGGACTCCAAAGTAGCCCTAGTCTACGGTCAGATGAATGAACCGCCGGGAGCTCGTATGAGAGTTGG
TCTGACTGCCTTAACTATGGCAGAATATTTCCGAGATGTTAATGAGCAAGACGTACTTCTATTTATCGACAATATCTTCC
GTTTTGTACAAGCAGGATCCGAGGTATCCGCTTTATTGGGTAGAATGCCTTCTGCTGTGGGTTACCAACCCACCCTTAGT
ACCGAAATGGGTTCTTTACAAGAAAGAATTACTTCTACGAAAAAAGGGTCCATAACCTCTATTCAAGCAGTTTATGTACC
TGCAGACGATTTGACTGACCCTGCTCCTGCCACCACATTTGCACATTTAGATGCGACTACCGTACTATCAAGAGGATTAG
CTGCTAAAGGTATCTATCCAGCGGTAGATCCTTTAGATTCAACGTCAACTATGCTACAACCTCGAATCGTTGGCGAGGAA
CATTATGAAACTGCGCAACAAGTAAAGCAAACTTTACAACGTTACAAGGAGCTTCAGGACATTATAGCTATCCTGGGGTT
GGACGAATTATCCGAAGAGGATCGCTTAACCGTCGCAAGAGCACGAAAGATTGAGCGTTTCTTATCACAACCTTTTTTCG
TAGCAGAAGTATTTACAGGTTCTCCGGGAAAATATGTTGGGCTAGCGGAAACAATTAGAGGGTTTAATTTGATCCTTTCC
GGAGAATTTGATTCTCTTCCTGAACAGGCCTTTTACTTAGTGGGTAACATCGATGAAGCTACTGCGAAGGCTACGAACTT
AGAAATGGAGAGT

Alignment

ORF - retro_brap_51 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.45 %
• Parental protein coverage: 77.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EVSHHLGQNVVRTIAMDGTEGLVRGRRVLNTGAPITVPVGRATLGRIMNVLGEPIDERGEIKTEHYLPIH
          EV...LG.N.VR..AM..TEGL.RG..V...G.P..VPVG.ATLGRI.NVLGEP.D..G...T....PIH
Retrocopy EVQQLLGNNRVRAVAMSATEGLKRGMDVVDMGNPLSVPVGGATLGRIFNVLGEPVDNLGPVDTLTTSPIH

Parental  RDAPALVDLATGQEILATGIKVVDLLAPYQRGGKIGLFGGAGVGKTVLIMELINNVAKAHGGFSVFAGVG
          ..APA..DL.T...I..TGIKVVDLLAPY.RGGKIGLFGGAGVGKTVLIMELINN.AKAHGG.SVF.GVG
Retrocopy KSAPAFIDLDTTLSIFETGIKVVDLLAPYRRGGKIGLFGGAGVGKTVLIMELINNIAKAHGGVSVFGGVG

Parental  ERTREGNDLYREMIESGVIKLGEKQSESKCALVYGQMNEPPGARARVGLTGLTVAEYFRDAEGQDVLLFI
          ERTREGNDLY.EM.ESGVI........SK.ALVYGQMNEPPGAR.RVGLT.LT.AEYFRD...QDVLLFI
Retrocopy ERTREGNDLYMEMKESGVIN-ELNLADSKVALVYGQMNEPPGARMRVGLTALTMAEYFRDVNEQDVLLFI

Parental  DNIFRFTQANSEVSALLGRIPSAVGYQPTLASDLGALQERITTTKKGSITSVQAIYVPADDLTDPAPATT
          DNIFRF.QA.SEVSALLGR.PSAVGYQPTL....G.LQERIT.TKKGSITS.QA.YVPADDLTDPAPATT
Retrocopy DNIFRFVQAGSEVSALLGRMPSAVGYQPTLSTEMGSLQERITSTKKGSITSIQAVYVPADDLTDPAPATT

Parental  FAHLDATTVLSRQISELGIYPAVDPLDSTSRMLSPHILGEEHYNTARGVKKVVQNYKNLQDIIAILGMDE
          FAHLDATTVLSR.....GIYPAVDPLDSTS.ML.P.I.GEEHY.TA..VK...Q.YK.LQDIIAILG.DE
Retrocopy FAHLDATTVLSRGLAAKGIYPAVDPLDSTSTMLQPRIVGEEHYETAQQVKQTLQRYKELQDIIAILGLDE

Parental  LSEDDKLTVARARKIQRFLSQPFHVAEIFTGAPGKYVDLKENINSFQGLLDGKYDDLPEQSFYMVGGIDE
          LSE.D.LTVARARKI.RFLSQPF.VAE.FTG.PGKYV.L.E.I..F...L.G..D.LPEQ.FY.VG.IDE
Retrocopy LSEEDRLTVARARKIERFLSQPFFVAEVFTGSPGKYVGLAETIRGFNLILSGEFDSLPEQAFYLVGNIDE

Parental  VVAKAEKISKEA
          ..AKA.....E.
Retrocopy ATAKATNLEMES

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_51 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,