RetrogeneDB ID: retro_obra_6

Retrocopy location

• Organism: Oryza brachyantha
• Coordinates: 7:40138..41881(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OB07G10090
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OB03G19880
• Aliases: None
• Description: None

Sequence

>retro_obra_6
ATGCCGGCGACGACGACCGACGGCACGACGGACCACGGCGGCAAACCGGCGGTAAGGAGCAAGACTGGGACGTGGCGGGC
GTGCCCGTTCATCCTGGGCAACGAGTGCTGCGAGCGCCTGGCCTACTACGGCATGAGCTCCAACCTCGTCAACTACATGG
TCGACCGCCTCCGCCAGGGCAACGCCGCCGCCGCCGCCAGCGTCAACAACTGGTCCGGCACATGCTACGTCATGCCCCTC
GTCGGGGCCTTCGTCGCCGACGCCTACCTCGGTCGCTACCGCACCATCGCCGCATTCATGGCGCTCTACATTCTCGGCCT
CGCGCTCCTCACCATCACTGCCTCCGTGCCCGGCATCAAGCCGCCCTACTGCGGAGGCGCAGTCGCACCCTCCGCTCCGT
GCGGGCCCTCCGGCGCCCAGACCGCCGCCTTCTTCGTCGCGCTTTACCTCATCGCCCTGGGCACCGGCGGGATCAAGCCC
TGCGTCTCCTCCTTTGGCGCCGACCAGTTCGACGACGCCGACCCGCGGGAGCACCGGAGCAAGGCCTCCTTTTTCAACTG
GTTCTACATGTCCATAAACGCTGGCGCCCTGGTCGCATCATCGATGCTCGTCTGGGTGCAGATGAACATCGGCTGGGGAT
GGGGCTTCGGCATCCCAGCGATCGCCATGGCAGTCGCCGTCGCCAGCTTCCTCCTGGGAAGCAAGCTCTACAGGCATCAG
AAGCCGGGGGGCAGCCCGCTCACCAGGATGCTGCAGGTGGTCGTGGCCGCAGCCAGGAAGTCACGAGTGGTGGCGCTGCC
CGCGGACGCCGCCCTCCTCTACGAGGGCGAGGGGGACAACAAGACCTCCTGCAGCGGCCGGAGGCGGGTGGCGCACACGG
ACCAGTTCAGGTGGCTTGACCGGGCGGCGGTGGGGACGGCCGAGGACGGCGGCGGCCCCTGGCGGCTGTGCCCGGTGACG
CAGGTGGAGGAGCTCAAGACGGTGGTGCGGCTGCTGCCGGTGTGGGCGAGCGGCATCGTGATGTCGGCGGTGTACGGGCA
GATGAGCACCATGTTCGTGCTGCAGGGCAACACGCTGGACCCTCGCATGGGCGCCTCCTTCAAGATCCCCTCCGCCTCGC
TCTCCATCTTCGACACCCTCAGCGTCATCGCCTGGGTCCCCGTCTACGATCGCCTCATCGTCCCCGCCGCCCGCCGCTTC
ACCGGCCACCCGCGCGGCTTCACTCAGCTCCAGCGCATGGGCATCGGCCTCGTCATCTCCGTCTTCTCCATGGTCGCCGC
CGGGGTGCTCGAGGTGGTGCGCCTCCGCGTCGCCGCCGCCCACGGCATGCTCGACTCCACAGACTATCTGCCCATCTCCA
TCTTCTGGCAGGTGCCGCAGTACTTCATCATCGGCGCCGCTGAGGTGTTCGCCTTCATCGGCCAGATCGACTTCTTCTAC
GACCAGGCGCCGGACGACATGCGCAGCATGTGCACCGCCCTGTCGCTCACCTCGTCGGCGCTCGGAAACTACCTCAGCAC
GCTGCTCCTAGTCATCGTCACGGCCGTCTCCACAAGGGGTGGCGGCGTCGGCTGGATCCCCGACAACCTCAACCGCGGCC
ACCTCGACTACTTCTTCTGGCTGCTCGCCGTGCTCAGTACCGTCAACTTCCTCGTCTACCTATGGATCGCCAAGTGGTAC
AGGTGCAAGACGGCCGCCACCACCACCGCGGCTAGTGATGAAGCAGACGCCCAAAACGCTTGA

Alignment

ORF - retro_obra_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.89 %
• Parental protein coverage: 95.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TGDGSVGFSGNPILKHETGNWRACSLILGTEVCERLAYYGISKSLVTYLSTRMHEGNVSAARNFTTWQGT
          T.DG.....G.P.....TG.WRAC..ILG.E.CERLAYYG.S..LV.Y...R...GN..AA.....W.GT
Retrocopy TTDGTTDHGGKPAVRSKTGTWRACPFILGNECCERLAYYGMSSNLVNYMVDRLRQGNAAAAASVNNWSGT

Parental  CYLTPLIGATLADSYWGKYQTIAVFSTIYFLGMAALTLSALIPSLQPPQCIGSFCPQ----PTMPQYLIY
          CY..PL.GA..AD.Y.G.Y.TIA.F...Y.LG.A.LT..A..P...PP.C.G...P.....P...Q....
Retrocopy CYVMPLVGAFVADAYLGRYRTIAAFMALYILGLALLTITASVPGIKPPYCGGAVAPSAPCGPSGAQTAAF

Parental  FVGLYMIALGSGGIKPCVSSFGADQFDDTDPAERTKKGAFFNWFYFAINIGSLISGTVLIWVQQNCGYGI
          FV.LY.IALG.GGIKPCVSSFGADQFDD.DP.E...K..FFNWFY..IN.G.L.....L.WVQ.N.G.G.
Retrocopy FVALYLIALGTGGIKPCVSSFGADQFDDADPREHRSKASFFNWFYMSINAGALVASSMLVWVQMNIGWGW

Parental  GFGIPTVFIAFAVGSFFIGSQIYRYQIPAGSPLIRVCQVVIAAMRK-RNVDLPVDSSLLYELHGKT-SAI
          GFGIP....A.AV.SF..GS..YR.Q.P.GSPL.R..QVV.AA.RK.R.V.LP.D..LLYE..G......
Retrocopy GFGIPAIAMAVAVASFLLGSKLYRHQKPGGSPLTRMLQVVVAAARKSRVVALPADAALLYEGEGDNKTSC

Parental  EGSRKLEHSSEFSFFDKAAIISWNERGGSHDPWRLCTITQVEELKILLRMFPIWATGIVFFTVCAQNSSM
          .G.R...H...F...D.AA.......GG...PWRLC..TQVEELK...R..P.WA.GIV...V..Q.S.M
Retrocopy SGRRRVAHTDQFRWLDRAAVGTAEDGGG---PWRLCPVTQVEELKTVVRLLPVWASGIVMSAVYGQMSTM

Parental  FIEQGMALDNQIG-SFKIPPATLSSLDVISIVVWVPIYESFVVPIASRLTGKERGFSELQRMGIGLFVST
          F..QG..LD...G.SFKIP.A.LS..D..S...WVP.Y....VP.A.R.TG..RGF..LQRMGIGL..S.
Retrocopy FVLQGNTLDPRMGASFKIPSASLSIFDTLSVIAWVPVYDRLIVPAARRFTGHPRGFTQLQRMGIGLVISV

Parental  TAVAAAALVELKRLEIARSEDLIHHKVPVPMSILWQAPQYLLIGIGEVFTSIGQAEFFYNQSPDSMRSLG
          ....AA...E..RL..A............P.SI.WQ.PQY..IG..EVF..IGQ..FFY.Q.PD.MRS..
Retrocopy FSMVAAGVLEVVRLRVAAAHGMLDSTDYLPISIFWQVPQYFIIGAAEVFAFIGQIDFFYDQAPDDMRSMC

Parental  SAFALVTVSLGSYLSSFILTLVSYFTSRGDNPGWVPDNLNEGHLDRFFWLIAGLSFFNLLLFIHYARQYK
          .A..L....LG.YLS...L..V.....RG...GW.PDNLN.GHLD.FFWL.A.LS..N.L.....A..Y.
Retrocopy TALSLTSSALGNYLSTLLLVIVTAVSTRGGGVGWIPDNLNRGHLDYFFWLLAVLSTVNFLVYLWIAKWYR

Parental  CKTA
          CKTA
Retrocopy CKTA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryza brachyantha was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza brachyantha was not studied using ChIP-Seq data.

EST

Oryza brachyantha was not studied using EST data.

TSS

Oryza brachyantha was not studied using FANTOM5 data.

Lab

retro_obra_6 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza brachyantha 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza brachyantha	OB03G19880	1 retrocopy	retro_obra_6 ,