RetrogeneDB ID: retro_brap_26

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A01:10843728..10846434(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra038498
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra010168
• Aliases: None
• Description: None

Sequence

>retro_brap_26
ATGGAGATGCATTCGAAAGTTCAGGTACGATCATCATCGGTTGTGGATATGGATCTAGACGTAATAGAAGAAACTGTAGA
TAGGTCTGTCTCGGAGGAGAAACCATCTCTCCGTTCCGTCTCTGTGAAATTCAAATTGAATATCGCCAAGAAAAGTTTTA
GGAAGAGAAGCAGACAAGAATCAGAGAAAGACGAAGAAGAAGATGAAGAAGACGGTAGGGTTTTAGGGAATTACGAGATA
GCGAGGCTAAGGGAAGAATCGAGACGAGAGTATCTGAAGATGAGGGAGAACAAGAAGGTGGAGGAGTTTAAGGAACAGGT
AGAGTTCGAGCTTTCGCTGTTTGAAGGCGTGAAGCTTACAGAGAAGGAAGAAATTGAGTTTAGGTACAAGAAGGAACTGT
ATAAGCTCTTGAACACAACGTGGGATGATGTTGGTTATTATAAGATTCCAGATGCCTATGATCAAGAAGGTGGTGTTGAT
CAGAGGAAGAGGTTTGCTGTGGCGAGGCAACGGTATGGTGAGGTGACGAGGGAGAAAGAAGCTTGGGAGGATCATCAGGC
TCAGAAGGCGACAGTTAGGTTTGGTGCTAAGGACAAGAAGCAAGTTTCTGATGGGTATGAGTTTGTGTTTGACGAGGTTA
CAAGCTTCGTTGAGACATCTGTGGAAGCTGAGAAAGACAGAGGTTATGATGAGAGAAGAGTTGCTAAAGATGATAGGAAG
ATGCTTCCTATATATGCCTACAGAGATGAGTTGCTGAAACTCGTTGAAGAGAATCAGGTTCTTGTGATTGTTGGGGAGAC
AGGGTCGGGCAAGACAACGCAGATACCGCAGTATCTTCAAGAAGCTGGCTACACTAAGCGTGGAAAGATCGGTTGCACTC
AGCCCCGGAGAGTTGCTGCAATGAGCGTTGCTGCCAGAGTGGCTCAAGAGTTAGGTGTAAAGCTAGGACATCAAGTTGGA
TACTCAATTAGATTCGAAGACTGTACTTCGGAGAAGACAGTTATCAAGTACATGACTGATGGGATGCTGTTGCGAGAGCT
TCTCATAGAACCGAAACTCGATAGCTACAGCGTCATCATAGTTGACGAGGCTCACGAAAGAACGTTGTCCACTGATATTC
TCTTTGGATTAGTGAAGGATTTAGCAAAGGCTAGGCCTGACCTGAGGCTGATCATCTCCAGCGCAACGCTCGAAGCTAAA
AAGTTCTCTGAGTATTTTGATTCGGCGAGGATCTACATGATCCCGGGGAGAAGATATCCAGTTGAGAAGCTCTTCCAGAG
ATGTCCTGAGCCTGACCGCTTGGAGACTGCGGTGCGCACTGTGTTTCAGATTCATCAGAGGGAGCCGCTCGGAGACGTTT
TGGTTTTCCTCACAGGTCAAGAAGAGATTGAAACAGCTGAGACGAAGTTGAAGGAAATGATGAAAGATTTGGGCTCAAAG
AGCTCTGAGATCATTATCTGCCCCATCTACTCAAATCTCCCGACCGAACTACAAGCAAAAGTGTTTGATCCGGCTCCTAA
AGGGACACGGAAAGTTGTCCTAGCGACTAATATTGCAGAAACGTCGTTAACCATTGAAGGGATTAGATACGTGGTTGATC
CAGGGTACTGCAAGATCAACTCATACAACCCAAAAACCGGAATGGAATCACTTCTCGAAACTCCCATCTCAAAAGCTTCC
GCAGAGCAACGAGCTGGCCGGTCCGGAAGGACCGGTCCGGGGAAGTGTTTCAGGCTGTACAACGTCAAGGACTTGGAGCC
CACAACGATACCCGAAGTGCAAAGAGCCAACCTTGCAAGCGTTGTACTTACTTTGAAGAGTCTTGGCATCGATGATGTCT
TCAACTTCGACTTCATGGATCCTCCACCTGAGAAGTCTCTAATGAAGGCTCTAGAGCTGCTCTACGCTCTTGGCGCTTTG
GATGGGAAAAGTTATATTACTAAGCTGGGAGAGAGGATGGTTGAGTTTCCCGTTGATCCAATGTTGTCAAAGATGATTGT
TGGTTCGGAGAAGTACAAGTGCTCGGCTGAGATCATCACTATAGCCGCCATGTTGTCTACAGGGAGCTCCATCTTTTACA
GACCTACCAGGAACCAACAGTATCTCGCAGACAATGCACGGATGAGTTTCTACACTGATAACGCCGGCGACCACATTGCC
TTGTTGAGGGTGTACAACTCGTGGAAGGAGATGAACTACTCGAGCCAATGGTGCTACGAGAACTACATTCAGAGCAAGAG
TATGAGGAGAGCTAGAGATATACGTGAACAGCTTGCTGGGCTTTTAAAGAGGATTGGAGTGGAACTGACTTCGAACTCTG
AGGATCTAGACGCGGTTAAGAAGGCGATACTGGCGGGTTTCTTTCCTCATTCCGCAAAGTTGCAGAAGGATGGATCGTAC
AGAAGAGTGAGGGAGCCTCAGACGGTTTATGTGCATCCTAGCTCAGGGTTGTTTGGGGCGTCCCCTAAGAAGTGGTTGGT
GTATCATGAGCTAGTACTTACTACCAAGGAGTATATGAGGCATACAACTGAGATGAAGCCGGAGTGGCTTGTTGAAATAG
CTCCACATTACTACAAGCTTAAAGACATTGAAGGGACTCGGACAAAGAAGAGTCAGAGCAGAAACATAAGATCCCTCATG
TTGATGGTTGATACTAACACGAAAGCTAAGAGGAAGGTTGATACTAACAAGAAAGCTAAGAGGTAA

Alignment

ORF - retro_brap_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.01 %
• Parental protein coverage: 60.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RKSLPIYGYREQLLQAVEEHQVLVIVGDTGSGKTTQIPQYLHEAGYTKRGKVGCTQPRRVAAMSVAARVA
          RK.LPIY.YR..LL..VEE.QVLVIVG.TGSGKTTQIPQYL.EAGYTKRGK.GCTQPRRVAAMSVAARVA
Retrocopy RKMLPIYAYRDELLKLVEENQVLVIVGETGSGKTTQIPQYLQEAGYTKRGKIGCTQPRRVAAMSVAARVA

Parental  QEMGVKLGHEVGYSIRFEDCTSDKTVLKYMTDGMLLRELLGEPDLASYSVVIVDEAHERTLSTDILFGL-
          QE.GVKLGH.VGYSIRFEDCTS.KTV.KYMTDGMLLRELL.EP.L.SYSV.IVDEAHERTLSTDILFGL.
Retrocopy QELGVKLGHQVGYSIRFEDCTSEKTVIKYMTDGMLLRELLIEPKLDSYSVIIVDEAHERTLSTDILFGLV

Parental  -DIARFRPDLKLLISSATMDAEKFSDYFDTAPIFSFPGRRYPVEINFTSAPEADYMDAAIVTVLTIHVRE
          .D.A..RPDL.L.ISSAT..A.KFS.YFD.A.I...PGRRYPVE..F...PE.D....A..TV..IH.RE
Retrocopy KDLAKARPDLRLIISSATLEAKKFSEYFDSARIYMIPGRRYPVEKLFQRCPEPDRLETAVRTVFQIHQRE

Parental  PLGDILVFLTGQEEIETAEEILKQRIRGLGTKIRELIICPIYANLPSELQAKIFEPTPEGARKVVLATNI
          PLGD.LVFLTGQEEIETAE..LK.....LG.K..E.IICPIY.NLP.ELQAK.F.P.P.G.RKVVLATNI
Retrocopy PLGDVLVFLTGQEEIETAETKLKEMMKDLGSKSSEIIICPIYSNLPTELQAKVFDPAPKGTRKVVLATNI

Parental  AETSLTIDGIKYVVDPGFSKMKSYNPRTGMESLLITPISKASATQRAGRAGRTSAGKCYRLYTAFNYNND
          AETSLTI.GI.YVVDPG..K..SYNP.TGMESLL.TPISKASA.QRAGR.GRT..GKC.RLY.......D
Retrocopy AETSLTIEGIRYVVDPGYCKINSYNPKTGMESLLETPISKASAEQRAGRSGRTGPGKCFRLYNV----KD

Parental  LEENTVPEVQRTNLASVVLALKSLGIHDLINFDFMDPPPAEALVKALELLFALGALNKLGELTKAGRRMA
          LE..T.PEVQR.NLASVVL.LKSLGI.D..NFDFMDPPP...L.KALELL.ALGAL......TK.G.RM.
Retrocopy LEPTTIPEVQRANLASVVLTLKSLGIDDVFNFDFMDPPPEKSLMKALELLYALGALDGKSYITKLGERMV

Parental  EFPLDPMLSKMIVVSDKYKCSDEVISIAAMLSVGGSIFYRP-KDKQVHADNARMNFHTGNVGDHIALLKV
          EFP.DPMLSKMIV.S.KYKCS.E.I.IAAMLS.G.SIFYRP....Q..ADNARM.F.T.N.GDHIALL.V
Retrocopy EFPVDPMLSKMIVGSEKYKCSAEIITIAAMLSTGSSIFYRPTRNQQYLADNARMSFYTDNAGDHIALLRV

Parental  YSSWKETNYSTQWCYENYIQVRSMKRARDIRDQLEGLLERVEIEISSNMNELDSVRKSIVAGFFPHTAKL
          Y.SWKE.NYS.QWCYENYIQ..SM.RARDIR.QL.GLL.R...E..SN...LD.V.K.I.AGFFPH.AKL
Retrocopy YNSWKEMNYSSQWCYENYIQSKSMRRARDIREQLAGLLKRIGVELTSNSEDLDAVKKAILAGFFPHSAKL

Parental  QKNGSYRTVKHPQTVHIHPNSGLSQVLP-RWVVYHELVLTSKEYMRQVTELKPEWLIELAPHYYQRKDVE
          QK.GSYR.V..PQTV..HP.SGL....P..W.VYHELVLT.KEYMR..TE.KPEWL.E.APHYY..KD.E
Retrocopy QKDGSYRRVREPQTVYVHPSSGLFGASPKKWLVYHELVLTTKEYMRHTTEMKPEWLVEIAPHYYKLKDIE

Parental  DDASKK
          ....KK
Retrocopy GTRTKK

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_26 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.

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA027162	1 retrocopy	retro_oind_65,
Brassica oleracea	Bo5g087070	1 retrocopy	retro_bole_7,
Brassica rapa	Bra000445	1 retrocopy	retro_brap_32,
Brassica rapa	Bra010168	1 retrocopy	retro_brap_26 ,
Brachypodium distachyon	BRADI1G61220	1 retrocopy	retro_bdis_4,
Glycine max	GLYMA06G21821	1 retrocopy	retro_gmax_7,
Leersia perrieri	LPERR08G09260	1 retrocopy	retro_lper_14,
Hordeum vulgare	MLOC_5589	1 retrocopy	retro_hvul_14,
Oryza meridionalis	OMERI08G09070	1 retrocopy	retro_omer_5,
Oryza nivara	ONIVA08G11780	1 retrocopy	retro_oniv_26,
Oryza punctata	OPUNC08G10350	1 retrocopy	retro_opun_23,
Oryza glaberrima	ORGLA08G0098600	1 retrocopy	retro_ogla_26,
Oryza rufipogon	ORUFI08G12410	1 retrocopy	retro_oruf_44,
Prunus persica	PRUPE_ppa000714mg	1 retrocopy	retro_pper_32,
Sorghum bicolor	Sb04g022460	1 retrocopy	retro_sbic_37,
Setaria italica	Si021302m.g	1 retrocopy	retro_sita_41,