RetrogeneDB - Retrocopy retro_hvul

                        
>retro_hvul_70
ATGTCGGTCTTAATCGTCACCAGCGTGGGCGATCTCGTGGTGGATCTCCACACCGATCGGTGCCCCCGCACCACCTACAA

CTTCCTCAAGCTCTGCAAGATGAAGTACTACAACGGGTGCCTGTTCCACAAGGTGGCCAAGGATTTCGTGGCACAGACCG

GGGACCCGACCGGGACCGGGACTGGCGGCGATTCGGTGTACAAGTTCCTCCACGGTGATCAGGCTCGATTCTTCGACGAC

GAGATCCACCCGGAACTGAGGCATTCGAAGATCGGCACCGTTGCCATGGCAAGCGCCGGCAAAAACCGCAACGCCGCGCA

GTTCTACATCACACTGCGGGACGACGTGGAATACCTTATGATAAACACACCGTGTTTGGGATAGTTGCTGAAGGTGAAGG

TCTTGACACGCTGACGAAGATAAACGAATCATATGTTGATGGCGATGGGAGACCATTCAAGGACATAAGGATTAAACATA

CATGTGTCTTGTACGACCCTGACGACGATCCTGCCCAGCTTGCTGAACTCATTCCTGCAAATTCTCCCGTTGGAAAGCCA

ATCGAGGAGATTTCAGAAGAGCGCTTAGAGGATACCTGGGTCCCTCTCGATGAAACAGTGGACCCTGTGCAGCTTGAGGG

GATGATCCGTTCGAAAGAAGCGCATACAAATGCCGTGATCCTTGCTAGTATTGGAGACATTCCAGATGCCGAGGTCAAGC

CACCAGACAATGTCTTGTTTGTCTGTCAACTCAACCCACTGACACAGGATGAGGACCTGTATACGATATTTTCTCGCTTC

GGAACGGTGACATCGGCCGAAACAATCCGTGACTACAAGACTGATCACAGCTTGTGCTATGCTTTTGTTGAGTTCGAAGC

AAAGGAAGCCTGCGAGCGTGCACACAGGGATATGAACAATTGTCTGATTGATGACCGGAGAATTCAAGTTGATTTTAGCC

AGAGCGTTTCAAAGCTGTGGCGTCAGTTCAGACAGGGCACTCGGAATGCAAATAAAGATGGGTGCTGCAAGAGTCATGCC

CCTGATTATCGAGCCCGAGATCGGGATAAGGGTGCTGAGAAGAAAAACAAAGGACCGAGATTATGTTCTGAAAGATGAAA

ACACTCAGCTAGGCGGCAGTAAACGTGGAAGTTATGATTTAGTCTTTGATGAGGACGGTGCT

ORF - retro_hvul_70 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	78.28 %
Parental protein coverage:	70.13 %
Number of stop codons detected:	0
Number of frameshifts detected:	2

Retrocopy - Parental Gene Alignment:

                                ParentalMSVLIVTSVGDIELDLHTDLCPLTTKNFLKLCKMKYYNGCLFHKVEKDFLAQSGDPTGTGSGGDSVYKFL
MSVLIVTSVGD...DLHTD.CP.TT.NFLKLCKMKYYNGCLFHKV.KDF.AQ.GDPTGTG.GGDSVYKFL
RetrocopyMSVLIVTSVGDLVVDLHTDRCPRTTYNFLKLCKMKYYNGCLFHKVAKDFVAQTGDPTGTGTGGDSVYKFL
ParentalYGDQARFFNDEIRPELRHSKTGTIAMASAGENCNASQFYITLRDDVDYLD-DKHTVFGTVAEG--LDTLT
.GDQARFF.DEI.PELRHSK.GT.AMASAG.N.NA.QFYITLRDDV.YL..DKHTVFG.VAEG..LDTLT
RetrocopyHGDQARFFDDEIHPELRHSKIGTVAMASAGKNRNAAQFYITLRDDVEYLM<DKHTVFGIVAEGEGLDTLT
ParentalKINEAYVDDKGRPFKDIRIKHTYILDDPFDDPPQLAEFIPENSPLGKPHDEVAEERLEDSWVPLDETVDP
KINE.YVD..GRPFKDIRIKHT..L.DP.DDP.QLAE.IP.NSP.GKP..E..EERLED.WVPLDETVDP
RetrocopyKINESYVDGDGRPFKDIRIKHTCVLYDPDDDPAQLAELIPANSPVGKPIEEISEERLEDTWVPLDETVDP
ParentalGQLEELIRSKEAHANAVILESVGDIPDAEVKPPDNVLFVCKLNPVTQDEDLYTIFSRFGSVTSAEIIRDF
.QLE..IRSKEAH.NAVIL.S.GDIPDAEVKPPDNVLFVC.LNP.TQDEDLYTIFSRFG.VTSAE.IRD.
RetrocopyVQLEGMIRSKEAHTNAVILASIGDIPDAEVKPPDNVLFVCQLNPLTQDEDLYTIFSRFGTVTSAETIRDY
ParentalKTGDSLCYAFIEFEAKEACERAYFKMDNCLIDDRRIHVDFSQSVSKLWGQFRQSKRNGNKDGCFKCGAPD
KT..SLCYAF.EFEAKEACERA...M.NCLIDDRRI.VDFSQSVSKLW.QFRQ..RN.NKDGC.K..APD
RetrocopyKTDHSLCYAFVEFEAKEACERAHRDMNNCLIDDRRIQVDFSQSVSKLWRQFRQGTRNANKDGCCKSHAPD
ParentalHIARDCDQDGEQKPKAP-NYVLKDDNTQRGGNNRRSYDFVFEDDTA
..ARD.D...E.K.K.P..YVLKD.NTQ.GG..R.SYD.VF..D.A
RetrocopyYRARDRDKGAEKKNKGP>DYVLKDENTQLGGSKRGSYDLVFDEDGA

                            

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

                        

RNA-Seq - click to see more details

Hordeum vulgare was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Hordeum vulgare was not studied using ChIP-Seq data.

EST - click to see more details

Hordeum vulgare was not studied using EST data.

TSS - click to see more details

Hordeum vulgare was not studied using FANTOM5 data.

Lab - click to see more details

retro_hvul_70 was not experimentally validated.

Retrocopy orthology:

Hordeum vulgare 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI1G20760	1 retrocopy	retro_bdis_34,
Aegilops tauschii	F775_03869	1 retrocopy	retro_atau_2,
Hordeum vulgare	MLOC_58863	1 retrocopy	retro_hvul_70 ,

	RetrogeneDB ID:	retro_hvul_70
Retrocopy location	Organism:	*Barley (Hordeum vulgare)*
	Coordinates:	4:447587876..447589058(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	None
	Ensembl ID:	MLOC_58863
	Aliases:	None
	Description:	None

Parental	MSVLIVTSVGDIELDLHTDLCPLTTKNFLKLCKMKYYNGCLFHKVEKDFLAQSGDPTGTGSGGDSVYKFL
	MSVLIVTSVGD...DLHTD.CP.TT.NFLKLCKMKYYNGCLFHKV.KDF.AQ.GDPTGTG.GGDSVYKFL
Retrocopy	MSVLIVTSVGDLVVDLHTDRCPRTTYNFLKLCKMKYYNGCLFHKVAKDFVAQTGDPTGTGTGGDSVYKFL

Parental	YGDQARFFNDEIRPELRHSKTGTIAMASAGENCNASQFYITLRDDVDYLD-DKHTVFGTVAEG--LDTLT
	.GDQARFF.DEI.PELRHSK.GT.AMASAG.N.NA.QFYITLRDDV.YL..DKHTVFG.VAEG..LDTLT
Retrocopy	HGDQARFFDDEIHPELRHSKIGTVAMASAGKNRNAAQFYITLRDDVEYLM<DKHTVFGIVAEGEGLDTLT

Parental	KINEAYVDDKGRPFKDIRIKHTYILDDPFDDPPQLAEFIPENSPLGKPHDEVAEERLEDSWVPLDETVDP
	KINE.YVD..GRPFKDIRIKHT..L.DP.DDP.QLAE.IP.NSP.GKP..E..EERLED.WVPLDETVDP
Retrocopy	KINESYVDGDGRPFKDIRIKHTCVLYDPDDDPAQLAELIPANSPVGKPIEEISEERLEDTWVPLDETVDP

Parental	GQLEELIRSKEAHANAVILESVGDIPDAEVKPPDNVLFVCKLNPVTQDEDLYTIFSRFGSVTSAEIIRDF
	.QLE..IRSKEAH.NAVIL.S.GDIPDAEVKPPDNVLFVC.LNP.TQDEDLYTIFSRFG.VTSAE.IRD.
Retrocopy	VQLEGMIRSKEAHTNAVILASIGDIPDAEVKPPDNVLFVCQLNPLTQDEDLYTIFSRFGTVTSAETIRDY

Parental	KTGDSLCYAFIEFEAKEACERAYFKMDNCLIDDRRIHVDFSQSVSKLWGQFRQSKRNGNKDGCFKCGAPD
	KT..SLCYAF.EFEAKEACERA...M.NCLIDDRRI.VDFSQSVSKLW.QFRQ..RN.NKDGC.K..APD
Retrocopy	KTDHSLCYAFVEFEAKEACERAHRDMNNCLIDDRRIQVDFSQSVSKLWRQFRQGTRNANKDGCCKSHAPD

Parental	HIARDCDQDGEQKPKAP-NYVLKDDNTQRGGNNRRSYDFVFEDDTA
	..ARD.D...E.K.K.P..YVLKD.NTQ.GG..R.SYD.VF..D.A
Retrocopy	YRARDRDKGAEKKNKGP>DYVLKDENTQLGGSKRGSYDLVFDEDGA

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

RetrogeneDB ID:

retro_hvul_70