RetrogeneDB ID:

retro_mdom_801

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:2:26959553..26961378(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SUPT5H
Ensembl ID:ENSMODG00000013570
Aliases:None
Description:suppressor of Ty 5 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:11469]


Retrocopy-Parental alignment summary:






>retro_mdom_801
TACCAGAAGACAGACAGCCCCCTGCTGATCAAGTCCGCGGTGGCCCCGGAGAACCTCAAGGGCTACATCTACGTGGAGGC
TTACAAGGCCAGCCACGTCCTGCAGGCCATCGAAGGCTTGGTCAGCCTGCGGCAGGGCCGCCTGCAGCAGCAGCAGCAGC
AGCAGGTGCCCATCGGGGAGATGACCGACGTGCTCAAGGTGCTGTCCAAGGAGGGCCCCATCCTGCAGCCCAAGAGCTGG
GTGCGCGTGAGGACAGGCCTGTACAGGGGTGACCTGGCTCAGGTGTCTCGGGTGGAGCCGGACCAAAGCAGCGTCTCCCT
CAAGCTGATTCCTCGAATCGACTACGGCCTCCTGGCGGGCGGCCAGCAGCCCCCAGAGGGCTTGGCCAAGAGGCGGAGGT
TCCAGCGAAGACCTCCGCAGCAGCTGCTGGATGCGCACAAGATTCGCTCTCTGGGCGGCAGGCTGACCTTCGATGGAGAT
TTCCTGGTCTTCGGGGGCAACCGCTACAGCCCCCGAGGCTTCCTGTTGAAGACCCTGAGCGTGTCGCGCGTCCTCCGAGA
GGGCGTGAAGCCCACGCTGGCCGAGCTGCAGCAGTTCGAGGAGCGGCCCGAGGCTCTGCAAGCCCTGCAGCTGGCCGCAG
AGGACAGCTCCGCGGAGCAGAGCTTCAGGCTCGGAGACAAGGTGGAAGTGAGCGGCGGGGAGCTCGTGCACCTGCGGGGC
CGGGTGGTGAGCGTGCAGGGCCCCCTGGTGCGGATGCTGCCCCAGCACGAGATGCTGCGCGAGGTGCTGGCGTTCCCCGC
CTGCGAGCTGCGCAAGCACTTCGAGGTCGGGGACCACGCCCAAGTGGTCTCGGGCCGCTCCCGCGGCAAGTCTGGCTTCG
TGCTGAGGGCCGAGGCCGCCTTTGTCCTGCTCTTCTGCGACCTCAACAAGGAGGAGCTCCGAGTCCTCCCCAGAGACCTG
CAGCTGCTCGGGAACACGGCCCCGGCGCTGGACCTGCTCATGCAGCAGCAACGCTGGGGCCAGCTGGTGCAGCTGCCGTC
CAACACGGTGGGCATCTTCGTGGGCCTGGACGACGCGGACACCTGCCGGGTGCTGGACATTCAGGGCAAGCTGCAGCTGG
TGCGCAGCCAGGCAGTCGCCGACAGGAAGCACAACCCGTTGGCCGTGGCCCTGGACTCGGGCCAGAACGAGCTTCGCCCC
CGGGCGCTGGTCAGGGTCCTGGAAGGTCCGCACTCGGGCCTCGAGGCCTGCATCCTCCACCTCTTCCAAGGCGTCGCCTT
CCTCCACTCCAAGAAGATCATGGACCACGGGGGCCTCTTCGTCTGCAAGACCCGCCACCTCCTGCTCAGCGAGGCCCCAC
GGGCCAAGGACCTCCCCTCCCGCGACTTGGCGCTGGGCGCCCCGCAGCCCTGCTCCCATCACTGCCAGGCCCCCTGGTGC
CCCCGCAGGGCCTAGGGACCCAGCGCTGGGGAGGGCAGCGGGTGCTGGCCCGGGCCAGGGCCGCAGAGTCAACGATCTGG
TGGGTCAGACTGTGCGCATCTGCCAGGGGCCCTACAAGGGCTACATGGGGATGGTGAAGGAGGCCACGGACTCTGTTGCT
CGGGTGGAGCTACACACCACGTGCCAGACGATTTCCGTGCAATCCCAGAGACTGGTCCGCCTAGGCACCCCGAGCTCCCA
ATCCCGTGACTCCACCCCTCACGCCACCCCCAGCTATGGCTCCCAGACACCCATCTACAACCTGGGCTCCTTTACCCCCC
TGTATGACTGCAGGACCCCCAAGGCCCAGGGGGACCAAACTCCAGATTCCAGGGCCTCCTCTCCT

ORF - retro_mdom_801 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 51.54 %
Parental protein coverage: 60.24 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalYVSSPQPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNL---RLGYWNQQMVPIKEMTDVLKVV-K
Y.....PL.IKS.VAPE..KGYIYVEAYK..HV.QAIEG...L...R........VPI.EMTDVLKV..K
RetrocopyYQKTDSPLLIKSAVAPENLKGYIYVEAYKASHVLQAIEGLVSLRQGRXXXXXXXXVPIGEMTDVLKVLSK
ParentalEVTNLKPKSWVRLKRGIYKDDIAQVDYVEPSQNTISLKMIPRIDYDRIKARMSLKDWFAKRKKF-KRPPQ
E...L.PKSWVR...G.Y..D.AQV..VEP.Q...SLK.IPRIDY.............AKR..F..RPPQ
RetrocopyEGPILQPKSWVRVRTGLYRGDLAQVSRVEPDQSSVSLKLIPRIDYGLLAGGQQPPEGLAKRRRFQRRPPQ
ParentalRLFDAEKIRSLGGDVASDGDFLIFEGNRYSRKGFLFKSFAMSAVITEGVKPTLSELEKFEDQPEGID-LE
.L.DA.KIRSLGG....DGDFL.F.GNRYS..GFL.K....S.V..EGVKPTL.EL..FE..PE....L.
RetrocopyQLLDAHKIRSLGGRLTFDGDFLVFGGNRYSPRGFLLKTLSVSRVLREGVKPTLAELQQFEERPEALQALQ
ParentalVVTESTGKEREHNFQPGDNVEVCEGELINLQGKILSVDGNKITIMPKHEDLKDMLEFPAQELRKYFKMGD
...E....E....F..GD.VEV..GEL..L.G...SV.G......P.HE.L...L.FPA.ELRK.F..GD
RetrocopyLAAEDSSAEQ--SFRLGDKVEVSGGELVHLRGRVVSVQGPLVRMLPQHEMLREVLAFPACELRKHFEVGD
ParentalHVKVIAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLCSETASGVD-VGGQHEWGELVQLDPQ
H..V..GR..G..G...R.E..FV.LF.DL...EL.VLPRDLQL...TA...D....Q..WG.LVQL...
RetrocopyHAQVVSGRSRGKSGFVLRAEAAFVLLFCDLNKEELRVLPRDLQLLGNTAPALDLLMQQQRWGQLVQLPSN
ParentalTVGVIVRL-ERETFQVLNMYGKVVTVRHQAVTRRKDNRFAVALDSEQNNIHVRDIVKVIDGPHSGREGEI
TVG..V.L....T..VL...GK...VR.QAV..RK.N..AVALDS.QN....R..V.V..GPHSG.E..I
RetrocopyTVGIFVGLDDADTCRVLDIQGKLQLVRSQAVADRKHNPLAVALDSGQNELRPRALVRVLEGPHSGLEACI
ParentalRHLFRGFAFLHCKKLVENGGMFVCKTRHLVLAGGSKPRDV--TNFTVGGFAPMS-PRISSPMHP-SAGGQ
.HLF.G.AFLH.KK....GG.FVCKTRHL.L.......D........G...P.S.P....P..P..AG..
RetrocopyLHLFQGVAFLHSKKIMDHGGLFVCKTRHLLLSEAPRAKDLPSRDLALGAPQPCS<PSLPGPLVP<PAGPR
ParentalRGGFGSAGGGGMSRGRGRRDNDLIGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLTT
....G.A.G.G...G.GRR.NDL.GQTVRI.QGPYKGY.G.VK.AT.S.ARVELH.TCQTISV..QRL..
RetrocopyDPALGRAAGAG--PGQGRRVNDLVGQTVRICQGPYKGYMGMVKEATDSVARVELHTTCQTISVQSQRLVR
ParentalVGSRRPGGMTSAYGRTPMYGSQTPMYVQGSRTPMYSSQTPLHDGDRTPHYGSQTP
.G........S....TP.YGSQTP.Y..GS.TP.Y...TP...GD.TP......P
RetrocopyLGTPSSQSRDSTPHATPSYGSQTPIYNLGSFTPLYDCRTPKAQGDQTPDSRASSP

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_801 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_801 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 ENSMODG00000013570 1 retrocopy
retro_mdom_801 ,


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