RetrogeneDB - Retrocopy retro_oruf

                        
>retro_oruf_19
ATGGCGAGCTGGGCATTGGCAATGGCGAGCTCGCCGATGGCCATGGACGCGGACAAGCTCAGCTACGAGATCTTCTCCCT

GCTGGAGAGCAAGTTCCTCTTCGGCGCCGGCGGCGGCGGGTGCCTGTCGTCGGGGCCGTGCACGCCGGCGAGGCCGTTTC

TTGGCGGCGGCGGCGGCATGGACGGGCGGGTGCGGGTGCTGGCCATCGACGGGTGCGGCTCGTCGGGCGCCGGGGACGCG

CTGCTCGCCGCGGCGGCGCTCGCGCGGCTGGAGGCCGGGCTGCGGAAGCGAACCGGGGACTCCGACGCCCGCGTCGCGGA

TTTCTTCGACGTCGCGGCGGGCGCCGGCGCCGGTGGGGTGCTCGCGGCGATGCTGTTCTTGAGGGGCCCCGACGGGAGGC

CGAGGTACACGGCGGAGGAGGCGCTTGAGTTCGTGGCTGCTAGCGTCGGGAGGGACTGGGCCGGCCGGCGCGGGCGGTGG

GCGCGGCTGTTCCGCGGCGGCGCGCGGGGGGCGGAGAGGTCGTTCCGGCGGGTGTTCGGCGACGCCACGCTCAAGGACAC

CGTCGCGCCGCTGCTCGTCCCGTGCTACGACCTCGCCACCGCCGCGCCTTTCATGTTCTCGCGCGCCGACGCCGTCGAGA

GCGACAGCTACGACTTCGCCCTCCGCGACGTCTGCGCGGCCACCTGCGCCGCCGGGAGCACGGCCGCCGCCGTCAGGTCG

GTGGACGGGCGCACCGCCATCGCCGCGGCTTCCGGCGGCGTGGCGGCCATGGGCAACCCGGCCGCGGCGGCCATCACGCA

CGTGCTCCACAACAAGCAGGAGTTCCCCCTCGCCACCACCGTCGACGACATCCTCGTCCTCTCCATCGGCACCGGCGCCT

CCACCTCCGCCACCGCGACGCCGATGCCCACGCGCTCCCCGTCGCCGCGCGAGATGGCGCGCGTCACCGCCGAGGGCGTG

GCGGACATGGTCGACGAGTCCGTCGCCATGGCGTTCGGCCACACGAGCGGGAGCAGCAGCAACTACGTGCGCATCCAGGC

CAGCAAGGCGGCGACCGCGCTCCACGGCGCCGCCGCCGCGGGCGCGATGCTGTCGCAGCGGAACGTGGAGTCCGTGCTGT

TCCGCGGGCGGAGGATGTCGGAGAGGACGAACGCCGAGAAGGTGGACGCCGCGGCGGCGGAGGTGGTGAAGGAGCACGAG

CGGCGGCGGCGCAGCCCGCTGCCGAACGTGGTGATCAAGCAGGTGGGCACGCCGCGGGTATCGTCGGCGACCACGGCGTC

GTCGGGGACGGCGAGGACGGCGGCGTCGACGTTGGCGTCGCCGGCGTCGTACGGCTCCCGCCAATAG

ORF - retro_oruf_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	54.14 %
Parental protein coverage:	76.89 %
Number of stop codons detected:	0
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalAAAAAAGQLDVDKLTYEIFSILESKFLFGYDDPKLVFSGGDEPQGAVKGTPARGPAVVERGKVCVLSIDG
A.A......D.DKL.YEIFS.LESKFLFG........SG...P.....G....G.....R..V......G
RetrocopyAMASSPMAMDADKLSYEIFSLLESKFLFGAGGGGCLSSGPCTPARPFLG---GGGGMDGRVRVLAIDGCG
ParentalGGRAADGLLAGAALVSLEASLRRRTGDETARLADFFDVAAGSGAGGVLAAMLVARGGDGRPMFSAEDALA
...A.D.LLA.AAL..LEA.LR.RTGD..AR.ADFFDVAAG.GAGGVLAAML..RG.DGRP...AE.AL.
RetrocopySSGAGDALLAAAALARLEAGLRKRTGDSDARVADFFDVAAGAGAGGVLAAMLFLRGPDGRPRYTAEEALE
ParentalFLMRSLRRGWSGGGGGGAAGGIRALFRRPGAAFRKVFGDLTLRDTVRPVLVPCYDLASAGPFLFSRADAV
F...S..R.W.G..G..A....R...R.....FR.VFGD.TL.DTV.P.LVPCYDLA.A.PF.FSRADAV
RetrocopyFVAASVGRDWAGRRGRWAR-LFRGGARGAERSFRRVFGDATLKDTVAPLLVPCYDLATAAPFMFSRADAV
ParentalETAAYDFRLRDVCAATCAGSDGSASAVEVRSSDGATRIAAVGGGL-ALGNPTAAAITHVLNNKREFPLAA
E...YDF.LRDVCAATCA.......A..VRS.DG.T.IAA..GG..A.GNP.AAAITHVL.NK.EFPLA.
RetrocopyESDSYDFALRDVCAATCA---AGSTAAAVRSVDGRTAIAAASGGVAAMGNPAAAAITHVLHNKQEFPLAT
ParentalGVEDLLVISIGSGECDN---RPTGGAAASTSEIVRIAAEGVADMVDQAVAMAFGH--NRTNNYIRIQAMG
.V.D.LV.SIG.G........P......S..E..R..AEGVADMVD..VAMAFGH......NY.RIQA..
RetrocopyTVDDILVLSIGTGASTSATATPMPTRSPSPREMARVTAEGVADMVDESVAMAFGHTSGSSSNYVRIQASK
ParentalSPRASRGGMRCG
...A..G....G
RetrocopyAATALHGAAAAG

                            

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

                        

RNA-Seq - click to see more details

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

ChIP-Seq - click to see more details

Oryza rufipogon was not studied using ChIP-Seq data.

EST - click to see more details

Oryza rufipogon was not studied using EST data.

TSS - click to see more details

Oryza rufipogon was not studied using FANTOM5 data.

Lab - click to see more details

retro_oruf_19 was not experimentally validated.

Retrocopy orthology:

Oryza rufipogon 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA009703	1 retrocopy	retro_oind_23,
Oryza glumaepatula	OGLUM03G36170	1 retrocopy	retro_oglu_8,
Oryza nivara	ONIVA03G37650	1 retrocopy	retro_oniv_28,
Oryza rufipogon	ORUFI03G37950	1 retrocopy	retro_oruf_19 ,

	RetrogeneDB ID:	retro_oruf_19
Retrocopy location	Organism:	*Brownbeard rice (Oryza rufipogon)*
	Coordinates:	3:23255263..23256610(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ORUFI03G28220
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	None
	Ensembl ID:	ORUFI03G37950
	Aliases:	None
	Description:	None

Parental	AAAAAAGQLDVDKLTYEIFSILESKFLFGYDDPKLVFSGGDEPQGAVKGTPARGPAVVERGKVCVLSIDG
	A.A......D.DKL.YEIFS.LESKFLFG........SG...P.....G....G.....R..V......G
Retrocopy	AMASSPMAMDADKLSYEIFSLLESKFLFGAGGGGCLSSGPCTPARPFLG---GGGGMDGRVRVLAIDGCG

Parental	GGRAADGLLAGAALVSLEASLRRRTGDETARLADFFDVAAGSGAGGVLAAMLVARGGDGRPMFSAEDALA
	...A.D.LLA.AAL..LEA.LR.RTGD..AR.ADFFDVAAG.GAGGVLAAML..RG.DGRP...AE.AL.
Retrocopy	SSGAGDALLAAAALARLEAGLRKRTGDSDARVADFFDVAAGAGAGGVLAAMLFLRGPDGRPRYTAEEALE

Parental	FLMRSLRRGWSGGGGGGAAGGIRALFRRPGAAFRKVFGDLTLRDTVRPVLVPCYDLASAGPFLFSRADAV
	F...S..R.W.G..G..A....R...R.....FR.VFGD.TL.DTV.P.LVPCYDLA.A.PF.FSRADAV
Retrocopy	FVAASVGRDWAGRRGRWAR-LFRGGARGAERSFRRVFGDATLKDTVAPLLVPCYDLATAAPFMFSRADAV

Parental	ETAAYDFRLRDVCAATCAGSDGSASAVEVRSSDGATRIAAVGGGL-ALGNPTAAAITHVLNNKREFPLAA
	E...YDF.LRDVCAATCA.......A..VRS.DG.T.IAA..GG..A.GNP.AAAITHVL.NK.EFPLA.
Retrocopy	ESDSYDFALRDVCAATCA---AGSTAAAVRSVDGRTAIAAASGGVAAMGNPAAAAITHVLHNKQEFPLAT

Parental	GVEDLLVISIGSGECDN---RPTGGAAASTSEIVRIAAEGVADMVDQAVAMAFGH--NRTNNYIRIQAMG
	.V.D.LV.SIG.G........P......S..E..R..AEGVADMVD..VAMAFGH......NY.RIQA..
Retrocopy	TVDDILVLSIGTGASTSATATPMPTRSPSPREMARVTAEGVADMVDESVAMAFGHTSGSSSNYVRIQASK

Parental	SPRASRGGMRCG
	...A..G....G
Retrocopy	AATALHGAAAAG

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

RetrogeneDB ID:

retro_oruf_19