RetrogeneDB ID: retro_obar_3

Retrocopy location

• Organism: Oryza barthii
• Coordinates: 7:12066739..12068125(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OBART07G12790
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OBART05G23750
• Aliases: None
• Description: None

Sequence

>retro_obar_3
ATGGCGGCGGCGCAGAGGGTGGTGGCGGAGCTGAGAGAGGCGTGCGCGACGCCGGCGGCGAGGCTGGCGGAGGTGGCCGC
GGCGATGGCCGGCGAGATGGAGGCCGGGCTGGCGGTGGAGGGCGGAAGCAGCGAGATGAAGATGATCGTGTCATACGTCG
ACACCCTCCCCACCGGCGGCGTGGAGGGGTCGTTCTACGCGCTCGACCTCGGCGGCACCAACTTCCGCGTCCTCCGCGTG
CGGCTTGCCGGCGGCGGCGTCGCCGAGCGCGTGGCGAGGGAGGTCCCGATCCCTCCCGGCCTCATGTCCGGCGGCGGCGC
AACCTCGGAGTGCCTCTTCGGCTTCATCGCCTCCGCGCTAGCCGAGTTCGTCGGCGAGGAGGAAGAAGAAGGCGGCCTCG
ACGGCGGCGAGAGGGAGCTTGGGTTCACCTTCTCCTTCCCAGTGCACCAAACCTCCATCGCGTCGGGGACGCTCATCCGG
TGGACGAAGGCGTTCGCCGTCGACGACGCGATCGGCGAGGACGTCGTGGCGGCGCTGCAGGCGGCCATGTCGGAGCGGGG
GCTCGACATGCGCGTGTCGGCGCTCATCAACGACACCGTCGGGACGCTCGCCGCGGGCAGCTACTACGACGAGGACGTCG
TGGCCGCCGTCATCCTCGGCACCGGCACGAACGCCGCCTACGTCGAGGACGCCACCGCCATCGCCAAGCTACACCCATCG
CAGCTTCCAGCATCGAACACCATGGTGATCAACACCGAGTGGGGCAGCTTCGCCTCGCCGTGCCTCCCATTGACGGAGTT
CGACGAAGCACTCGATCAGGAGAGCCTCAACCCCGGCGAGCAGACCTACGAGAAGCTCATCTCCGGGATGTACCTCGGCG
AGATCGTCAGGAGGGTCCTCCTCAAGATCTCCTCCCGGTGCCCCTCCCTCCTCGGCGGCGCCGGCGAGCTCGCGACGCCG
TTCGTCCTCAGGACACCCGACGTGTCCGCGATGCACCACGACGAGACGCCCGACCTGAGCATCGTCGGCGAGAAGCTGGA
ACGCACGCTGGGCATCCGCGGCACGTCGCCGGAGGCGAGGAGGATGGTCGTCGAGGTGTGCGACATCGTCGCCACGAGGG
CCGCCCGGCTGGCCGCTGCGGGGATCGTCGGGATCCTGAAGAAGATCGGGAGGGTCGACGGCGGCGAGGGGCGGAGGAGG
AGGTCGGTGGTCGCCGTGGACGGCGGGCTGTTCGAACACTACGGCAAGTTCCGGCGGTGCATGGAGAGCGCGGTGAGGGA
GCTGCTCGGAGAGGCGGCGGCGGAGAGGGTGGTCGTCAAGCTCGCCAGCGACGGCTCCGGGCTCGGCGCCGCCCTGGTTG
CAGCTGCTCACTCGCAGAGAGCATAA

Alignment

ORF - retro_obar_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.53 %
• Parental protein coverage: 98.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVEMHAGLASEGGS-KLKMIISYVDALPSGEEKGVFYALDLGGTNFRVLRVQLGGKEGRVIKQEHDEIS
          MA.EM.AGLA.EGGS...KMI.SYVD.LP.G...G.FYALDLGGTNFRVLRV.L.G..G.V......E..
Retrocopy MAGEMEAGLAVEGGSSEMKMIVSYVDTLPTGGVEGSFYALDLGGTNFRVLRVRLAG--GGVAERVAREVP

Parental  IPPHLMTGG---SNELFDFIASSLAKFVASEGEDFHLAEGRQRELGFTFSFPVKQTSIASGTLINWTKGF
          IPP.LM.GG...S..LF.FIAS.LA.FV..E.E...L..G..RELGFTFSFPV.QTSIASGTLI.WTK.F
Retrocopy IPPGLMSGGGATSECLFGFIASALAEFVGEEEEEGGL-DGGERELGFTFSFPVHQTSIASGTLIRWTKAF

Parental  SIDETVGEDVVTELTKALERQGLDMKVTALINDTIGTLAGGRYDDNDVIAAVILGTGTNAAYVERANAIP
          ..D...GEDVV..L..A....GLDM.V.ALINDT.GTLA.G.Y.D.DV.AAVILGTGTNAAYVE.A.AI.
Retrocopy AVDDAIGEDVVAALQAAMSERGLDMRVSALINDTVGTLAAGSYYDEDVVAAVILGTGTNAAYVEDATAIA

Parental  KWH-DLLPKSGDMVINMEWGNFRSSHLPLTEFDQALDAESLNPGEQVYEKLISGMYLGEIVRRVLLKMAE
          K.H...LP.S..MVIN.EWG.F.S..LPLTEFD.ALD.ESLNPGEQ.YEKLISGMYLGEIVRRVLLK...
Retrocopy KLHPSQLPASNTMVINTEWGSFASPCLPLTEFDEALDQESLNPGEQTYEKLISGMYLGEIVRRVLLKISS

Parental  EA-SLFGDEVPPKLKIPFIIRTPYMSMMHCDRSPDLRTVGAKLKDILGVQSTSLKTRRLVVDVCDIVAKR
          ...SL.G......L..PF..RTP..S.MH.D..PDL..VG.KL...LG...TS...RR.VV.VCDIVA.R
Retrocopy RCPSLLGG--AGELATPFVLRTPDVSAMHHDETPDLSIVGEKLERTLGIRGTSPEARRMVVEVCDIVATR

Parental  AACLAAAGIHGILKKLGR-DVPNTDKQRTVIAVDGGLYEHYTIFAECVESTLRDMLGEEVSSTIVIKLAK
          AA.LAAAGI.GILKK.GR.D.......R.V.AVDGGL.EHY..F..C.ES..R..LGE......V.KLA.
Retrocopy AARLAAAGIVGILKKIGRVDGGEGRRRRSVVAVDGGLFEHYGKFRRCMESAVRELLGEAAAERVVVKLAS

Parental  DGSGIGAALLAAAHSQ
          DGSG.GAAL.AAAHSQ
Retrocopy DGSGLGAALVAAAHSQ

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza barthii was not studied using ChIP-Seq data.

EST

Oryza barthii was not studied using EST data.

TSS

Oryza barthii was not studied using FANTOM5 data.

Lab

retro_obar_3 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza barthii 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA017675	1 retrocopy	retro_oind_38,
Oryza barthii	OBART05G23750	1 retrocopy	retro_obar_3 ,
Oryza glumaepatula	OGLUM05G25120	1 retrocopy	retro_oglu_6,
Oryza nivara	ONIVA05G24490	1 retrocopy	retro_oniv_15,
Oryza rufipogon	ORUFI05G25500	1 retrocopy	retro_oruf_35,