RetrogeneDB ID:

retro_mdom_40

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:X:22631737..22633252(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000025325
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000000740
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_40
GAAGGCATCATGGAAAAGCTGCTCGCCAAAGCCCCGGCCAGGGCGGCCGGCCCCGAAGACTCGGCCCTCGACAGCCTGGC
GCTGGCCAATGAAATCCTCGCCGACATCCATCCTCTGCGGAGCGCCGACGAAAACGTGGCGGAGCTGCTGCGGATCCTGA
AGGAGCCCCACTTTCGGGCTCTCCTGGAGGCCCGCGACACCCTGGCGTCCGAGGGCTACGAGCCGCCCCCGGCCTCCTCC
GACAGCCCCCTGCCCCCGGAGGACGCGGTCCAGCTGCTGAGCATCCACAAGCGAGCCGGGGAGCCCCTGGGGGTGACCCT
CCGGGTGGAGAACAACGACCTGGTGATCGCCCGCATCCTGCGCGGCGGAGTGATAGACCGCGGGGGGCTCCTCCGCGTGG
GGGACGTCATCAAGGAGGCCGACGGCCGCCGGGTGGGCACCGACGCCGGGGGGCTGCAGGAGCTGCTCAGGACCGCCGGG
CGCGACGTCCTGCTGAAGATCCTGCCCAGCTCCCGCAGAGCCACGAGCCCGCAGGACATGTTCGTGAAGTGCCACTTCGA
CTACGACCCCGGCGCCGACAGCCTCATCCCCTGCCAGGAGGTGGGCCTGAGCTTCTCCAGGGGGGACGTCCTGCAGATCG
TCAACACGGACGACCCCAACTGGTGGCAGGCGAGGCACGCCGAGGAAGGGAGCAGCACCGCCGCCGGCCTGGTGCCCAGC
CAGACTCTGGAGGAGAAGAGGAAGGCATTCGTCCGCTGTGGCAGGAGCAGCCCCGAGCCCCTGTGCGGGGCTGCCGGCAG
CCAGAAGAAGAAGAGGCGGATCATGTACGACACCCACCGCAACGCCGACTTCGACCGCCATGAGATCCAGATCTACGAGG
AGGTGGTGCGGGCGCCACCCTTCCAGCGCAAGGTCCTGGTGCTGATCGGGGCCCAGGGCGTGGGCCGCAGGACCCTGAAG
AACATCCTCATCGTGCTCAACCCCAGCCTGTTCGGGACCACCGTGCCCTTCACCTCCCGGAAGCCCAGGAAAGGGGAAGA
CGAGCAGGTGTACCGCTTTGTGAGCCGGCCTGAGATGGAGGCTGACATCAGGGCCGGCAGGTACCTGGAGTACGGGGAGT
ACCAGGGCAACCTGTACGGCACCAAGACCGAGTCCATCTTCGAGGTCACCCAGGCCGGGAAGACGTGCATCCTGGACGTG
AACCCGCGGGCCCTGAAGCTGCTCCGCACCGCCGACTTCATGCCCTACGTGGTGTTCATCGCCGCCCCCAAGCTGGACAT
CCTCCGCGCCATGCACGAGGCCACAGTGAATTCGGGGATCACCACCAAGCTGCCCACACAAGCCATGCTGCAGAGAACCG
TCAGCGAGAGCGGCCACATCCAGGGCACCTACAGCCACTACTTCGACTTGACCATCGTCAACGATGACCTGGACAAGGCC
TTCGAGAAGCTGCTGGCTGCCTTCGAGAGGCTGCGCACCGAGCCCCAGTGGATCCCCGTCAGCTGGCTGTACTAG

ORF - retro_mdom_40 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.7 %
Parental protein coverage: 81.32 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalARLLALFSSGQLAKELGLRDPSPPRGLSGRGRPSLPRLLPMDAIRILGIHKKAGEPLVRVTFRVEKKHLV
A.LL...........L..RD.....G.......S...L.P.DA...L.IHK.AGEPL..VT.RVE...LV
RetrocopyAELLRILKEPHFRALLEARDTLASEGYEPPPASSDSPLPPEDAVQLLSIHKRAGEPL-GVTLRVENNDLV
ParentalIARILHGSMIQRQGLLHLGEVIQEVKRHQVGSNPQELQELLPSISGSVTLQILPSYRDAVTPQQVFVKCH
IARIL.G..I.R.GLL..G.VI.E.....VG.....LQELL......V.L.ILPS.R.A..PQ..FVKCH
RetrocopyIARILRGGVIDRGGLLRVGDVIKEADGRRVGTDAGGLQELLRTAGRDVLLKILPSSRRATSPQDMFVKCH
ParentalFDYDPYNDNLIPCKEAGLKFSKGEILQIVNREDPNWWQANHVKEGGS--AGLIPSQFLEEKRKAFVRRDW
FDYDP..D.LIPC.E.GL.FS.G..LQIVN..DPNWWQA.H..EG.S..AGL.PSQ.LEEKRKAFVR...
RetrocopyFDYDPGADSLIPCQEVGLSFSRGDVLQIVNTDDPNWWQARHAEEGSSTAAGLVPSQTLEEKRKAFVRCGR
ParentalDSPGPFCGTISS-KKKKKMMYLTTRNAEFDRHEIQIYEEVAKMPPFQRKTLVLIGAQGVGRRSLKNRFIV
.SP.P.CG...S.KKK...MY.T.RNA.FDRHEIQIYEEV...PPFQRK.LVLIGAQGVGRR.LKN..IV
RetrocopySSPEPLCGAAGSQKKKRRIMYDTHRNADFDRHEIQIYEEVVRAPPFQRKVLVLIGAQGVGRRTLKNILIV
ParentalLNPSRFGTTVPFTSRKPREDEKDGQAYKFVSRAEMEADIKAGKYLEHGEYEGNLYGTRIDSILEVAQTGR
LNPS.FGTTVPFTSRKPR..E.D.Q.Y.FVSR.EMEADI.AG.YLE.GEY.GNLYGT...SI.EV.Q.G.
RetrocopyLNPSLFGTTVPFTSRKPRKGE-DEQVYRFVSRPEMEADIRAGRYLEYGEYQGNLYGTKTESIFEVTQAGK
ParentalTCILDVNPQALKVLRTSEFMPYVVFIAAPELETLRAMHKAVVDAGITTKLLTDTNLKKTVDESARIQRAY
TCILDVNP.ALK.LRT..FMPYVVFIAAP.L..LRAMH.A.V..GITTKL.T...L..TV.ES..IQ..Y
RetrocopyTCILDVNPRALKLLRTADFMPYVVFIAAPKLDILRAMHEATVNSGITTKLPTQAMLQRTVSESGHIQGTY
ParentalNHYFDLIIVNDNLDKAFEKLQAAIERLRAEPQWVPISWVY
.HYFDL.IVND.LDKAFEKL.AA.ERLR.EPQW.P.SW.Y
RetrocopySHYFDLTIVNDDLDKAFEKLLAAFERLRTEPQWIPVSWLY

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 0 .00 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_40 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_40 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Monodelphis domestica ENSMODG00000000740 1 retrocopy
retro_mdom_40 ,


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