RetrogeneDB ID:

retro_mdom_1364

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:4:152936129..152937542(-)
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:ENSMODG00000010436
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_1364
GTTAAGGTTTCCACTAAATCCAATAGTACTGCTACTTCCCAGAACAAAACAACTTTTCAGTGTTCTGGGAAAAAGCAAGT
TGACTTTATCCAAAACAAGGAGAAAGAAGCCATTGTTAGAACCTTTTTCTAACCTACTATCTAAGTTACTATCTAAAGAG
AGCCTAATAAAGATAGTACCTCTACCAATGCCAGTACTACCAAATGTCAAGATAAACCTGAATTCTGGTAAAAAAGAAAA
TAAAGCACAATCAAAATGTAGGACTTCTGGAGCGGCAACTACTCATATTTCTGAAGTAAAACCTGCTTCATCTTTCAGTA
CCAAATTCAGGGAGGATTCCAAAATTGGTGATAAGAGAAGATACACTTGAATAAAAGTGCCAATTAGTACAGAAGAACTG
CCTTAACCAAAGAATCAGCAGAAGAGAAAAGAGCTTGTTTGGTTGAGTGGCAAAATGACAAAAGAAGAGTAATTAAAAGA
TCATCTACAACTGGTCTGCCTGTTCCACCTGCTCCACCCAACATGGAACTGCCAAAAGAAAAACCAGTTGAATCTTTCTG
GACTACCATTGCAGAAGATGAACAAAGATTATTCACTGATAAACTTAACAAAATATTTTTTGAATATTTGAACTTAATTA
ATAAGGGATGTCCATGAGGAGAAGTACTTTTAACACTAAAAGAGCTCATTGTAAAAATTCCAGATGCCAAGAAACTTATT
AAGTATCGGGTATGCCTTGCATGCCTTGAACCAATTACAAGCCCTATTGAAAATATCATAGCAATATATGAAGAAGCCAT
TCTTGCTGGAGCTCAGCCTATGGAAGAAATGCAACATGCGCTTGCAGATATCCTAACAATGAAGAGTCAAGTGAAGGGTA
ATGATGGGGAGAATATTGATGAGGTTTGTTCGGCTAATGAAGAGGCCAAAAAAATATGTGATGAACTTATACATCAGGAT
AAAGTTGATGTAGATGGGACATCAACAGAGGAAAATTCAGAATCAAAAGATAAAGATCATGAAACAAGGAATGTAAAACT
ACAGATGTTTGAAAGAGAGCAAGAGGATAAAGCAGAAGATTCAACAAGTGTTTTAGAGACTCCTGATAAGGAAACCAGCG
GGTCTTATGTCATTAAATATAATGTGTCAACTACTCCATCTTTGCCAAGTGTGAAACAGAAGATGAATTTTGATGAAAAT
ACTGCTTCATTTAAAGACGTGAAGTTTCTGACACCAGTGAGGCATTCTCGACGTCTGCAGGAGAAGTTTTGTAAATGACC
AGATATGTTAAATGATCATTATCCCTGTGTTTCTTCACTGGAACAGTTAGCAGAACTGGGAAGTGAAACCACTGCCTATA
TATGCCGTCCAAATACTGCATTATATACAACTTCCCTTGAAGAAGAAGCAAAA

ORF - retro_mdom_1364 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.02 %
Parental protein coverage: 66.48 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVSVSTKSNSTTTSQNKTAFQHSGKKQVDFIQN-KEKEAIVRNSTNVT---IRREPNKKIVPLSKPVLPNV
V.VSTKSNST.TSQNKT.FQ.SGKKQVDFIQN...K........N........E...KIVPL..PVLPNV
RetrocopyVKVSTKSNSTATSQNKTTFQCSGKKQVDFIQN>RRKKPLLEPFSNLLSKLLSKESLIKIVPLPMPVLPNV
ParentalKTNLNSGKKENEVQSKCRTSGAATTHVSEAKPASSFSTRFREDSKIVDKRRYTLTKAPISTG-RTALTKE
K.NLNSGKKEN..QSKCRTSGAATTH.SE.KPASSFST.FREDSKI.DKRRYT..K.PIST..RTALTKE
RetrocopyKINLNSGKKENKAQSKCRTSGAATTHISEVKPASSFSTKFREDSKIGDKRRYT*IKVPISTE<RTALTKE
ParentalSAEERRARLVEWQNDKRRVIKRSSTTGLTVPPAPPAPSNIELPKEKPLESFWTTIAEEDEQRLFTDKVNK
SAEE.RA.LVEWQNDKRRVIKRSSTTGL.VPPAPP...N.ELPKEKP.ESFWTTIAE.DEQRLFTDK.NK
RetrocopySAEEKRACLVEWQNDKRRVIKRSSTTGLPVPPAPP---NMELPKEKPVESFWTTIAE-DEQRLFTDKLNK
ParentalIFSEYLNLINKGCPREEVLLTLKELIVKIPDAKKLVKYWVCLARLEPITSPIENIIAIYEEAILAGAQPM
IF.EYLNLINKGCP..EVLLTLKELIVKIPDAKKL.KY.VCLA.LEPITSPIENIIAIYEEAILAGAQPM
RetrocopyIFFEYLNLINKGCP*GEVLLTLKELIVKIPDAKKLIKYRVCLACLEPITSPIENIIAIYEEAILAGAQPM
ParentalEEMRHALADILTMKSQVKGNDGENVDEVCSANEEIKKLCDEVLNQDKVDVDEASAEENSESKDKDHNTKN
EEM.HALADILTMKSQVKGNDGEN.DEVCSANEE.KK.CDE...QDKVDVD..S.EENSESKDKDH.T.N
RetrocopyEEMQHALADILTMKSQVKGNDGENIDEVCSANEEAKKICDELIHQDKVDVDGTSTEENSESKDKDHETRN
ParentalVKLQMVEREQEDKAEDSTSVLETPDKETSGSYVIKYNVSTTPYLQSVKKKMNFDENSASFKDLKFLTPVR
VKLQM.EREQEDKAEDSTSVLETPDKETSGSYVIKYNVSTTP.L.SVK.KMNFDEN.ASFKD.KFLTPVR
RetrocopyVKLQMFEREQEDKAEDSTSVLETPDKETSGSYVIKYNVSTTPSLPSVKQKMNFDENTASFKDVKFLTPVR
ParentalRSRRLQEKFCKLPDMLKDHYPCVSSLEQLAELGSESSAYICRPNTALCTTSLEEEIK
.SRRLQEKFCK.PDML.DHYPCVSSLEQLAELGSE..AYICRPNTAL.TTSLEEE.K
RetrocopyHSRRLQEKFCK*PDMLNDHYPCVSSLEQLAELGSETTAYICRPNTALYTTSLEEEAK

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_1364 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1364 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 11 parental genes, and 13 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000058981 retrocopy
retro_cfam_968,
Choloepus hoffmanni ENSCHOG000000099052 retrocopies
retro_chof_1493, retro_chof_973,
Cavia porcellus ENSCPOG000000123821 retrocopy
retro_cpor_171,
Felis catus ENSFCAG000000100211 retrocopy
retro_fcat_1770,
Myotis lucifugus ENSMLUG000000001321 retrocopy
retro_mluc_1515,
Monodelphis domestica ENSMODG00000010436 1 retrocopy
retro_mdom_1364 ,
Mustela putorius furoENSMPUG000000179961 retrocopy
retro_mputfur_1270,
Mus musculus ENSMUSG000000377251 retrocopy
retro_mmus_2651,
Otolemur garnettii ENSOGAG000000084281 retrocopy
retro_ogar_1743,
Tupaia belangeri ENSTBEG000000058071 retrocopy
retro_tbel_176,
Tursiops truncatus ENSTTRG000000096242 retrocopies
retro_ttru_1491, retro_ttru_1741,


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