RetrogeneDB ID:

retro_hvul_6

Retrocopy
location
Organism:Barley (Hordeum vulgare)
Coordinates:3:463920060..463922079(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:MLOC_60699
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:MLOC_56180
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_hvul_6
ATGGGGATCTCCGTCGCCGTCCCCTCCCTCCTCCTCCTCTCCGCCGCCCTCCTCCTGCCGCCGGCAGCTGCGGGATTCTC
CTTCACCTACAACTTCACCGCCGTCTCGGACTCGGCCCCATCGGGCATCTCCTTCCAGGGCGACGCCTTCTTCAACAAGT
TCATCCGCCTCACCCGCGACGAGCGCGTCGGGCCCCTCACCAGCAGCGCCGGCCGGGCCTTCTTCTCCCGCCCCATCCCA
CTCTTTGACCCTGTCTCCCGCCGCCCCGCCTCGTTCGCCTCCGCCTTCTCCTTCTCCATCTCCGCCCCCGAACCCTCCGC
CGCCTCCGGCGACGGCCTCGCCTTCTTCCTCTCCCCGTTCCCCTCAGTCCTCCCCAACAGATCCGCTGGCGGCCTTCTCG
GGCTCTTCAACTCCTCCGCCCGCAACGGGGGTCGCTCCCTCGTCGCCGTCGAATTCGACACCTACAGGAACGATTGGGAT
CCCAGCGACGACCACGTCGGCATCGACCTCGGGGGCATCGCCTCCGTGGCCACCGCCGACTGGCCGACCAGCATGAAGGA
CGGCCGCACGGCGCACGCGCGCGTCGCGTACGACGCTGAGGCCAAGAACCTCACCGTGGCCCTCTCCTACGGCGACGCTC
CCCCCACGGACGTCCTTCTGTGGTACGCCGTCGATTTGAGGGAACACCTGCCTGACTCCGTGGCCGTTGGCTTCTCCGCC
GCCACTGGCGAGGCCGCCGAGCTGCACAAGGTCCTGTACTGGGATTTCACCTCCAGCGTCGACAGCAAAGAGCAGACGGT
GATGCTGTGGGTGATATTGGGATTGTGCGGATTCCTTGTTGTGCTGGTCGGTGCAGGGGTTGTTTGGTTCGTCAAGGAAT
GGAGGAAGACAGGGGAATGTGTGCCCTATGTCGACATCGACGATGCAATGGGGTACGACGAGCTAACTGACGAGTTCATC
GTGCAGAGCGGGCCAAGACGGTTCCGTTATGCTGAATTGGTGGCGGCAACCAACAATTTCTCCGAGCAGAGGAAGCTCGG
GCAGGGCGGGTTCGGTGCTGTTTACCGGGGGTTCTTGAAGGAGCTCCGTCAGGAGGTGGCCATCAAGAGGGTCTCCAAGG
GGTCGACGCAGGGGCGCAAGGAGTACGCAGCCGAGGTACGCATCATCAGCCAGCTGCGCCACCGGCATTTGGTCCGGCTT
GTCGGGTGGTGCCATGAACACCGTGGTGACTTCTTGCTCGTCTATGAGCTCATGCCCAATGGCAGCGTCGACCAGCACCT
CTACGGCAAAGGCGTGCACCTCACCTGGCCGACACGGTATGACATTGCACTGGGCCTCGCGTCGGCATTGCTCTACCTCC
ACGAGGAGTGCCTTCAGTGCATCGTGCACCGCGACATCAAGCCGAGCAATGTGATGCTGGATGCCACCTTCAGTGCCAAG
CTCGGCGACTTTGGCCTTGCCAAGCTAGTTGAGCATGGCAGCCAGCCCTACACCACCGTCCTGGCTGGCACGTTAGGCTA
CTTGGCGCCAGAGTGCCTGACGACAGGCAAGGCAAGCCGGGAATCGGACGTGTACAGCTTCGGCGTCGTGGCACTGGAGA
TTGCTTGCGGACGACAGCCATCGGAGCCCACGGCGGAGCCGAGCAAGGCAAGGCTGGTGCCGTGGGTGTGGGAGCTTTAT
GGGAAGAAAGCCCTTCTCGAAGCGGCGGACTGGAGGTTGAAGGGGGAGTTTGACGAGAAGCAGATGGAGCATCTGATGGT
GGTCGGACTATGGTGCGCTCATCCGGACTACACGCATAGGCCAAGCATCAGGCAGGCCCTGAATGCCCTGAAATTTGAGG
CGCCATTGCCTGTGCTAGCGCCGAAGATGCCGGTGCCGACGTTCTTCCCTTTGCCTGACTTGGCTGCTCTGGTATCATCA
GTTGGAGGTGCGCAGAACCCAGGCGTTACTGAGTGCGAGTCATCAGGGGCTAATGCTGGCCAACGGTCTTCGGTGAGGGA
TAGACTTCTGGAGCCATGA

ORF - retro_hvul_6 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 54.57 %
Parental protein coverage: 66.72 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVDLRNVGLPQEAAVGFSASIGDLVEKHQILSWSFQSSMTDSKTKGTSLIAGLVSSGLLILLAIAVWLGYR
VDLR...LP...AVGFSA..G...E.H..L.W.F.SS..DSK.....L....V..GL...L...V..G..
RetrocopyVDLRE-HLPDSVAVGFSAATGEAAELHKVLYWDFTSSV-DSKEQTVML---WVILGLCGFLVVLVGAGVV
ParentalQYVKRKGKNIHDNIPEDADETPLDDQDMDSELEKGTAPRRFSYSELWRATRGFSDDEKLGEGGFGAVYRG
..VK...K......P...............E......PRRF.Y.EL..AT..FS...KLG.GGFGAVYRG
RetrocopyWFVKEWRKT-GECVPYVDIDDAMGYDELTDEFIVQSGPRRFRYAELVAATNNFSEQRKLGQGGFGAVYRG
ParentalFLHDRGLHVAIKRVSKMSSQGRREYIAEVTTIGRLRHRNLVQLVGWCHK-ADELLLIYELMTNGSLDVHL
FL......VAIKRVSK.S.QGR.EY.AEV..I..LRHR.LV.LVGWCH......LL.YELM.NGS.D.HL
RetrocopyFLKELRQEVAIKRVSKGSTQGRKEYAAEVRIISQLRHRHLVRLVGWCHEHRGDFLLVYELMPNGSVDQHL
ParentalYKSRDILTWPIRYKITLGMGHALMYLHQEWEQCVVHRDIKPSNVMLDSSFDARLGDFGLARLVDHSRGAH
Y.....LTWP.RY.I.LG...AL.YLH.E..QC.VHRDIKPSNVMLD..F.A.LGDFGLA.LV.H.....
RetrocopyYGKGVHLTWPTRYDIALGLASALLYLHEECLQCIVHRDIKPSNVMLDATFSAKLGDFGLAKLVEHGSQPY
ParentalTTMLAGTKGYMDPQCAVTSRASAETDVYSFGVVLLEIACGRRPVIQELEDESRMVLVEWVWALYGRGALL
TT.LAGT.GY..P.C..T..AS.E.DVYSFGVV.LEIACGR.P........S...LV.WVW.LYG..ALL
RetrocopyTTVLAGTLGYLAPECLTTGKASRESDVYSFGVVALEIACGRQP-SEPTAEPSKARLVPWVWELYGKKALL
ParentalDAVDARLDGEFDAREMERTLLVGLWCVHPDYGFRPSIRQAMSVLQFEAPLPELPPEMPVALLYVLP
.A.D.RL.GEFD...ME....VGLWC.HPDY..RPSIRQA...L.FEAPLP.L.P.MPV.....LP
RetrocopyEAADWRLKGEFDEKQMEHLMVVGLWCAHPDYTHRPSIRQALNALKFEAPLPVLAPKMPVPTFFPLP

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_6 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Hordeum vulgare MLOC_56180 1 retrocopy
retro_hvul_6 ,


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