RetrogeneDB ID:

retro_mdom_243

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:1:579593974..579597247(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000009906
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:ATP2B1
Ensembl ID:ENSMODG00000009874
Aliases:None
Description:ATPase, Ca++ transporting, plasma membrane 1 [Source:HGNC Symbol;Acc:814]


Retrocopy-Parental alignment summary:






>retro_mdom_243
CCCTCGGGTCCATCACCGGCCCGGGCAGGTTCCGCGAGTTTATCTCAGTTACAAGAGAGGCTGCTGCAGGTGAGCTTGAA
GGACCTGGGGCAGTTAATGAGATTACGGGGCTTGGAAGCGTTGGAGCAGCTGGAGGCGCACTTCGGAGGCGTTTCTGGGT
TGTGCCTGCTACTGCAGACGAACCCCGAGTTCGGGCTCCCCCTGGACCCTGTCGAACTGAGCCGTAGGCGAGAACAGTTC
GGCACCAATGAGGTGCCAAAACCCCGGGGCAAATATTTTTTGGAACTGGTATGGGACTCGCTGCAGGACACTACGCTCAT
TTTCCTGGAGGTGGCCGCTGTACTGTCACTAGCCGTGGCCTTCTATGAGCTCAAGATCAACAGAGAGACCAAAGGTTGCG
ACGTTGGCGGGGTCGTAGCAGGCTCTGAGAAGGAGGCAGAAGATGAGTTGGTAAGGTGGCTGGAGGGCACTGTCCTGCTG
ATATCCGTGGCTTTGGTGGTTCTGGCCACAGCCTTAAGTGACTGGAACAAGGAAAAGCAGTTCAGGAATCTGGAAGACCG
AGTGGTCCAAAGTCAGAAAGGAAAGGTATTTCGGAATGGCCAGATCCTGGAGGTACCTGTCAAGGACATCGTGGTGGGTG
ACGTGGTCCCGGTGTCATATGGGGATATGCTGCCTGCAGATGGGGTATTACTCCATGGGCTAAACTTAAAAATGGACGAG
AGTTCCTTGACCGGAGAACTGAACATGGTGAATAAGTCCTTGGACCGGGACCCAATTCTTCTGTCTGGAACCTACGTGAG
GGAGGGCTGGGGCAAAATCATAGTAACAGCTGTAGGGCCCAATTCACAAACTGGGATCATCCTGACCTTGCTTGATGCTA
GTGCCCAGCAAGGAAACCTGGAAGCTCAGAGGAAAGCGCAGCAGTGGGAAAGTCATTGCAAAAGTATATTAAAACTAAAA
CATTCTTACTCCAAAGAAAAGTTAGTGCTACAAAAGAAACTGTCAAAATTAGCAGTTTTGATTACAAAGTGTAGTATGCT
TATGGCTTCAATCACAGTAGTCACCCTTGTGACTCACTTTGTCATTAATACTTTTGTGATCGAGGGACAAAAATGGACTT
TGGATTGTACTTCAGTTTATACCCGATACTTTATTAAATTTTTCATTATTGGAATAACAATCTTGGTGGTGTCTATACCT
GAAGGTCTTCCTCTTGCAGTTACACTGTCTTTGGCTTACTGGGTAAAGAGAATGATGAAGGACAATAACCTAGTAAGGCA
TTTGGATGTTTATGAGTCAGTAAGAAATGCCACAACTATTTGTTTAGACAAAACTGGAACGCTGACCATGAACAGAATGA
CTGTAGTCCAAGCGTATATTGGTGAGAATCATTACCAAAGGCTTCCCAAAACCAATTCTATCCCAGACCCCATCCTGGAG
TACCTTTTAAAAGGTATTACTATTAATTGTTCTTATACTTCCAATGTCATTCTTCCCAAAGGTGGTCAGAAGTCAGTACA
ACAAATTGGCAATAAGACCGAATGTGCCTTATTGGGATTTCTCCTGCATTTGGACTTGGATTATGAAACAGAAAGAAACA
AAATACCACAGCAGAGTTTGTATAAAGTATATACCTTCAACTCAGATAGAAAATACATGAGCACTGTATTAAAATTGTCC
AGCGGAGGTTTCCTGATGTTTAGTAAAGGTCGTTCTGAAATAGTATTAGAGAAGTGTTGTAAAATCCTGGACAAAATGGG
AGAGCCTGTGGAATTGACAGAAACCAAAAAAGAAGAGATCTTTCATAATATTATTGAGCCAATGACTTCTGAGGGACTTC
AAACCATTTGTCTAGCCTTCAGAGAATTCTCAGACCAGGAAATGGAACCAGACTGGGACAGAGAAGAGGATATCATTACA
GAACTTACTTGTATTGCCCTTGTAGGCATTGAAGATCCTGTTAGACCTGAGGTTCCAAGTGCCATTAAGGAATGCCAGCA
AGCTGGAATTACTGTACGGATGGTCACTGGGGATAACCTCAATACTGCACGGGCTATAGCATTCAAATGTGGCATCTTGA
ACCTCCATGACAATTATTTGTCTCTAGAAGGCAGAGATTTCAATAGACTAATACGTAATAAATATGGGAAGATTGAACAG
ACACTTTTAGATAAGATTTGGCCAAGGCTTCGTGTGCTTGCAAGCTCTTCCCCCTCTGACAAGTACGCTCTTGTAAAGGG
TATAATTGACAGTGATGTTTTGGGAGTGAGGCAGATTGTAGCTGTAACCGGGGATGGCACTAATGATGGCCCAGTGTTAA
AAGTGGCAGATGTTGGGTTTGCCTTGGGTATCATTGGAACAGATATCGCTAGAGAAGCTTCAGACATCATTCTCATGGAC
GAGAACTTCACAAGCATTATGAAAGCAATTATGTGTGGAAGGAGCATTTATGACAACATCTCCAAGTTCCTCCAGTTTCA
GCTTACTCTTAGTATAGTAGCAACAACAGTGGCTTTTATAGGGGCATGTGTGACACAGGATTCACCATTTAAAGCGGTAC
AAATGCTATGGATTAACCTCATAATGGATACATTTGCTTCCTTGGCCTTAGTCACTGAAAAGCCAACAAAGACGCTTCTG
CTAAGAGACTTTCCTGAAAAGAAACAGCATCTCTTGTCCAGCTCCATGGTAAAGTATATTTTGGGCCATGCAGTGTACCA
GCTTACAGTCACTTTTGTTCTTATGTTTGTTGGTGAAGAGCTGTTTGGTTTTGAGAGTGGAAGAAAAGCTCTTCTCCACG
CCTCTCCTTCTACCCACTACACAATGATTTTCAACACTTTCGTTATGATGCAACTTTTCAATGAAATTAATGCCCGAAAG
ATTCATGGGGAGAGAAATGTTTTGGAAGGAATGCGTAGCAATAATTTCTTTTGCATCATTGTGGGGGGAACCTTTGCCTT
TCAGTTCCTCATTGTACAATTTGGTGGAAATATTTTCTGTTGTACCAGTCTTAGTCCAGACTTGTGGCTGTGGTGCATTT
TCCTAGGAGCAGGGATATTAGTGTGGGGTCAGTTTGTAACCAACATTCCCAACAAGTGTGTGGAACCCCTCATCAGGTTG
ATGGGTGGGAGATCAGAAGAAAAGGTTGAGACTATATGTCCTACAATATCAATGACTGAGGACCTGTGGTGGGTTCAGAA
CCCAAGCAGAATCCAGAATCAGAAAAGACTCATAAAAACATATCATTCTTACTTTCGTAGGAGTTTGTCCCAA

ORF - retro_mdom_243 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.59 %
Parental protein coverage: 61.65 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKEKSVLQGKLTKLAVQIGKAGLLMSAITVIILVLYFVIDTFWVQKRPWLAECTPIYIQYFVKFFIIGVTV
KEK.VLQ.KL.KLAV.I.K...LM..ITV..LV..FVI.TF......W...CT..Y..YF.KFFIIG.T.
RetrocopyKEKLVLQKKLSKLAVLITKCSMLMASITVVTLVTHFVINTFVIEGQKWTLDCTSVYTRYFIKFFIIGITI
ParentalLVVAVPEGLPLAVTISLAYSVKKMMKDNNLVRHLDACETMGNATAICSDKTGTLTMNRMTVVQAYINEKH
LVV..PEGLPLAVT.SLAY.VK.MMKDNNLVRHLD..E...NAT.IC.DKTGTLTMNRMTVVQAYI.E.H
RetrocopyLVVSIPEGLPLAVTLSLAYWVKRMMKDNNLVRHLDVYESVRNATTICLDKTGTLTMNRMTVVQAYIGENH
ParentalYKKVPDPDAIPASILSCLVTGISVNCAYTSKILPPEREGGLPRHVGNKTECALLGLVLDLKRDYQDVRNE
Y...P....IP..IL..L..GI..NC.YTS....P..........GNKTECALLG..L.L..DY...RN.
RetrocopyYQRLPKTNSIPDPILEYLLKGITINCSYTSNVILPKGGQKSVQQIGNKTECALLGFLLHLDLDYETERNK
ParentalIPEEALYKVYTFNSVRKSMSTVLKNSDGSYRIFSKGASEIILKKCFKILSANGEAKVFRPRDRDDIVKTV
IP...LYKVYTFNS.RK.MSTVLK.S.G....FSKG.SEI.L.KC.KIL...GE...........I....
RetrocopyIPQQSLYKVYTFNSDRKYMSTVLKLSSGGFLMFSKGRSEIVLEKCCKILDKMGEPVELTETKKEEIFHNI
ParentalIEPMASEGLRTICLAFRDFPAGEPEPEWDNENDIVTGLTCIAVVGIEDPVRPEVPDAIRKCQRAGITVRM
IEPM.SEGL.TICLAFR.F...E.EP.WD.E.DI.T.LTCIA.VGIEDPVRPEVP.AI..CQ.AGITVRM
RetrocopyIEPMTSEGLQTICLAFREFSDQEMEPDWDREEDIITELTCIALVGIEDPVRPEVPSAIKECQQAGITVRM
ParentalVTGDNINTARAIASKCGILHPGEDFLCLEGKDFNRRIRNEKGEIEQERIDKIWPKLRVLARSSPTDKHTL
VTGDN.NTARAIA.KCGIL......L.LEG.DFNR.IRN..G.IEQ...DKIWP.LRVLA.SSP.DK..L
RetrocopyVTGDNLNTARAIAFKCGILNLHDNYLSLEGRDFNRLIRNKYGKIEQTLLDKIWPRLRVLASSSPSDKYAL
ParentalVKGIIDSTVSEQRQVVAVTGDGTNDGPALKKADVGFAMGIAGTDVAKEASDIILTDDNFTSIVKAVMWGR
VKGIIDS.V...RQ.VAVTGDGTNDGP.LK.ADVGFA.GI.GTD.A.EASDIIL.D.NFTSI.KA.M.GR
RetrocopyVKGIIDSDVLGVRQIVAVTGDGTNDGPVLKVADVGFALGIIGTDIAREASDIILMDENFTSIMKAIMCGR
ParentalNVYDSISKFLQFQLTVNVVAVIVAFTGACITQDSPLKAVQMLWVNLIMDTLASLALATEPPTESLLLRKP
..YD.ISKFLQFQLT...VA..VAF.GAC.TQDSP.KAVQMLW.NLIMDT.ASLAL.TE.PT..LLLR..
RetrocopySIYDNISKFLQFQLTLSIVATTVAFIGACVTQDSPFKAVQMLWINLIMDTFASLALVTEKPTKTLLLRDF
ParentalYGRNKPLISRTMMKNILGHAFYQLVVVFTLLFAGEKFFDIDSGRNAPLHAPPSEHYTIVFNTFVLMQLFN
......L.S..M.K.ILGHA.YQL.V.F.L.F.GE..F...SGR.A.LHA.PS.HYT..FNTFV.MQLFN
RetrocopyPEKKQHLLSSSMVKYILGHAVYQLTVTFVLMFVGEELFGFESGRKALLHASPSTHYTMIFNTFVMMQLFN
ParentalEINARKIHGERNVFEGIFNNAIFCTIVLGTFVVQIIIVQFGGKPFSCSELSIEQWLWSIFLGMGTLLWGQ
EINARKIHGERNV.EG...N..FC.IV.GTF..Q..IVQFGG..F.C..LS...WLW.IFLG.G.L.WGQ
RetrocopyEINARKIHGERNVLEGMRSNNFFCIIVGGTFAFQFLIVQFGGNIFCCTSLSPDLWLWCIFLGAGILVWGQ
ParentalLISTIPTSRLKFLKEAGHGTQKEEI
....IP......L.....G...E..
RetrocopyFVTNIPNKCVEPLIRLMGGRSEEKV

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






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain 0 .00 RPM 0 .00 RPM
SRP007412_cerebellum 0 .00 RPM 0 .00 RPM
SRP007412_heart 0 .00 RPM 0 .00 RPM
SRP007412_kidney 0 .00 RPM 0 .00 RPM
SRP007412_liver 0 .00 RPM 0 .00 RPM
SRP007412_testis 353 .97 RPM 0 .00 RPM

ChIP-Seq - click to see more details

Monodelphis domestica was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mdom_243 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_243 was not experimentally validated.

Retrocopy orthology:
Monodelphis domestica 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
Macropus eugenii ENSMEUG000000142961 retrocopy
retro_meug_716,
Monodelphis domestica ENSMODG00000009874 1 retrocopy
retro_mdom_243 ,
Pelodiscus sinensis ENSPSIG000000054411 retrocopy
retro_psin_48,


Copyright © RetrogeneDB 2014-2017