RetrogeneDB ID:

retro_ppat_11

Retrocopy
location
Organism:Moss (Physcomitrella patens)
Coordinates:DS544895.1:3266664..3268872(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:PP1S6_407V6
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:PP1S45_94V6
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ppat_11
ATGGCAGTTCCAACCATTCCTAGTCCAGCCTGTATCTCGCAGTCGGCTAATGGGTCCATTATCTCAACGCGACGTTCGAC
TGAAACCAACCCTCGACAGCATCCGTCGACTTCTTATCGATGCGCTGGAAGAGTAGTTAGGAGACAAGGTAGGAGCGCAA
TTAGCAGGTCTGGAAGCAGGTATTTACATGATTTAGAGGCCGGTCGTTCACTGCTGAAAAGGGTTACTCTGAGAAGAGAT
TGGGATTCTAGGTTGGATGAGAAAGACCAATATCCCAGGCTTGGTGCAAGAGCGGCTGCGACGTTTGAAGCAAAACCTGA
AAATGCTGAGAAAGATTATTCTAAAAATGGGAAAGCTGCCAATAAAGGTGTGGACAATGGGAAGGATCGATTAGCTAAAG
TTCCAATCTCGAACATCAGAAACTTTTCTATCATCGCACATATTGATCATGGGAAATCAACATTAGCCGACAAGTTGCTG
CAGACCACTGGCACCGTTCTTGCGCGAGAAATGAAGGAGCAGTTTCTCGACAACATGGACCTTGAACGAGAGAGGGGTAT
TACCATTAAGCTTCAAGCAGCTCGTATGCGCTATGTGGATGAAACCGGTGAGGCTTACTGCCTGAATTTGATTGATACTC
CGGGCCATGTGGACTTCTCGTATGAGGTGTCCAGGTCTCTGGCAGCTTGTGAAGGTGCCCTCTTGGTGGTGGATGCTTCT
CAAGGAGTAGAAGCTCAAACCTTAGCCAACGTGTATTTAGCCCTCGAATCAAACCTAGAAATTATCCCTGTGCTCAACAA
GATCGACCTTCCTGGGGCTGACCCTGAGCGCGTGCGGAGGGAGATTGAGGAGATAATAGGCTTGGATTGTAGTGAAGCCA
TTTTGTGTTCTGCAAAGGAGGGAGTTGGAATTCCCGAGATCTTGAACGCAGTGGTTAAGAAGATTCCCCCACCGAAAGAC
ACAGCCGCAGAGCCTCTTCGCGCATTGATATTCGATTCCTACTACGATTCCTATCGGGGAGTTGTCGTGTACTTCAGAGT
GATGGATGGAAGGGTGAAGAAAGGGGACTACGTTCAGTTCATGAACAGCAAGACCGAGTATCAGGTGGACGAGGTAGGAG
TTTTGTCTCCTATTCAAATGCCAGTGAATGAGTTATACGCTGGTGAGGTGGGTTACTTGTCAGCATCCATCAAATCCGTG
GCTGACGCAAGAGTTGGGGATACTATTACTACAGTTTCTCGGAAAGCTGCCCAGGCTCTACCTGGGTACCAGTTGGCTAC
TCCTATGGTGTTCTGTGGGCTGTTTCCCATCGACGCAGATCAATTTGTAGAGCTTCGAGAAGCCCTCGAAAAGTTGCAGT
TAAACGATGCAGCACTGCAATTTGAGCCAGAGACATCCAGTGCGATGGGCTTTGGTTTCCGATGTGGGTTTCTGGGTCTC
CTGCACATGGAGATCGTGCAGGAAAGACTGGAAAGAGAGTACGGCCTCGACCTCATCACCACTGCTCCCAGTGTGGTGTA
TCGTGTCCATTGCACCGATGGCACTATAACTGAATGTTCAAATCCTTCTGCTTTGCCAGATGCTGGAAAACGCAAATCCA
TCGAGGAGCCATACGTAAGAATAGAGCTTCTCACGCCGAAGGACTATATAGGTCCTTTGATGGAACTAGCACAAGAAAGG
CGTGGAGAGTTCAAGGAAATGAAATTCATTACAGAGAACCGGGCTTCGTTGGTGTACATGTTGCCCTTGGGAGAAATGGT
AGGTGACTTTTTTGATCAGCTGAAGTCACGTAGCAAAGGCTACGCAAGCATGGAGTACTCTGTCAAGGGTTATCGAGAAA
GCAAGTTGGTGAAGCTCGACATTAGGATTAATGATGAGGCTGTCGACCCCCTTGCGGTCATTGTGCACCAGGATAAGGCT
TACAGTGTTGGCCGGGCACTTACTCAACAACTGAAGAAGTTGATTCCCCGTCAGCTGTTCAAGATCCCAATCCAAGCCTG
CATCGGCTCAAAGGTGATTGCTAGTGAGAATATTGCAGCCATGCGCAAAGACGTTCTTGCAAAATGTTATGGTGGAGACA
TTAGTCGGAAGAAGAAGTTGCTGAAAAAGCAAGCTGAGGGTAAGAAGCGCATGAAGTCATTGGGCAGGGTGGATGTTCCT
CAAGACGCTTTTATGGCCATCCTAAGGTTGGAGAAAGAAGTCGTGTAA

ORF - retro_ppat_11 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 50.28 %
Parental protein coverage: 78.36 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRSKKTGGANERFLLNLIDTPGHVDFSYEVSRSLAACQGVLLLVDAAQGVQAQTVANFYLAFESDLAIIPV
R........E...LNLIDTPGHVDFSYEVSRSLAAC.G.LL.VDA.QGV.AQT.AN.YLA.ES.L.IIPV
RetrocopyRMRYVDETGEAYCLNLIDTPGHVDFSYEVSRSLAACEGALLVVDASQGVEAQTLANVYLALESNLEIIPV
ParentalINKIDQINADPEGVKSQLKQIFDIDPESVLLTSAKTGLGLENILPAVIERIPQPKGLVDASLRMLLLDSY
.NKID...ADPE.V......I...D.....L.SAK.G.G...IL.AV...IP.PK......LR.L..DSY
RetrocopyLNKIDLPGADPERVRREIEEIIGLDCSEAILCSAKEGVGIPEILNAVVKKIPPPKDTAAEPLRALIFDSY
ParentalYDEYRGVICHVAVVDGVLKRGDKIESAATRQSYEIMEVGILYPELTNTGILLTGQVGYVVTGMRSTKEAR
YD.YRGV.....V.DG..K.GD..........Y...EVG.L.P.......L..G.VGY......S...AR
RetrocopyYDSYRGVVVYFRVMDGRVKKGDYVQFMNSKTEYQVDEVGVLSPIQMPVNELYAGEVGYLSASIKSVADAR
ParentalIGDTLFH-TRSVVEPLPGFKPARHMVFAGVYPADGSDYEALSSAVERLTCNDASVSIAKETSGALGIGFR
.GDT.....R.....LPG...A..MVF.G..P.D......L..A.E.L..NDA......ETS.A.G.GFR
RetrocopyVGDTITTVSRKAAQALPGYQLATPMVFCGLFPIDADQFVELREALEKLQLNDAALQFEPETSSAMGFGFR
ParentalCGFLGLLHMDVFHQRLEQEHGAQVITTTPTVPYIFEYSDGSKLTIQNPAALPSNPKSRLVACYEPTVMAT
CGFLGLLHM.....RLE.E.G...ITT.P.V.Y.....DG......NP.ALP...K.......EP.V...
RetrocopyCGFLGLLHMEIVQERLEREYGLDLITTAPSVVYRVHCTDGTITECSNPSALPDAGKRKSIE--EPYVRIE
ParentalIITPSEYVGSLMTLCSERRGQQTEYSFIDGQRAMLKYRMPLREVVIDFYNELKSITSGYASFDYEEAPYQ
..TP..Y.G.LM.L..ERRG...E..FI...RA.L.Y..PL.E.V.DF...LKS...GYAS..Y....Y.
RetrocopyLLTPKDYIGPLMELAQERRGEFKEMKFITENRASLVYMLPLGEMVGDFFDQLKSRSKGYASMEYSVKGYR
ParentalESDLVKLDILLNGQPVDALASICHRSKAHYVGRELCEKLKKVLDRQMFEVAIQAAIGAKVVARETLPALR
ES.LVKLDI..N...VD.LA.I.H..KA..VGR.L...LKK...RQ.F...IQA.IG.KV.A.E...A.R
RetrocopyESKLVKLDIRINDEAVDPLAVIVHQDKAYSVGRALTQQLKKLIPRQLFKIPIQACIGSKVIASENIAAMR
ParentalKNVLAKCYGGDVSRKRKLLEKQKEGKKRMKRVGNVDIPQEAFHSLLK
K.VLAKCYGGD.SRK.KLL.KQ.EGKKRMK..G.VD.PQ.AF...L.
RetrocopyKDVLAKCYGGDISRKKKLLKKQAEGKKRMKSLGRVDVPQDAFMAILR

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






RNA-Seq - click to see more details

Physcomitrella patens was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Physcomitrella patens was not studied using ChIP-Seq data.

EST - click to see more details

Physcomitrella patens was not studied using EST data.

TSS - click to see more details

Physcomitrella patens was not studied using FANTOM5 data.

Lab - click to see more details

retro_ppat_11 was not experimentally validated.

Retrocopy orthology:
Physcomitrella patens 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
Physcomitrella patens PP1S45_94V6 1 retrocopy
retro_ppat_11 ,




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