RetrogeneDB ID:

retro_mdom_1109

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:3:132091797..132093209(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CCNT2
Ensembl ID:ENSMODG00000000727
Aliases:None
Description:cyclin T2 [Source:HGNC Symbol;Acc:1600]


Retrocopy-Parental alignment summary:






>retro_mdom_1109
CTTACTGCCTTTTGCCTTCAATATAAACCAACAGTGACAGCATGTTTGTGCATTCACTTGTCCTGCAAGTGGTCCAATTG
GGAGATTCCTGTATCTACTGATTGAAAGCATTGGTGTGAATATGTGAATCCATCAGTTACCTTAGAATTACTAGATGAAT
TGACTCACAAGTTCCTACAAATTTTGTAGAAAACTCCTAATAGATTGAAGAGGATATGGAAATGAAGGGCTAATCAGGTG
GCTAGAAAATCAAAAGGGGATGGACAGGTGTCTAAAACAGCTCTTCTTGGTTCATCTCTGGCACAGAATTCCATTTTAGT
AGCTAGTGTTACTCATGTGACTGCAAATGCAAGCTTTCAAAAACCATCTATCTCAGCATTTCCTGCTCCAGTACCTCTGA
ATTCAGGAAATATTTCTGTTCAGGATAGTCATACATCTGATAATTTGGCAATACTAATGACAGGAATGCAAAGTACCTCA
TACAGTTTGGGATCACACCAAGAATGGCCTCAACATCAAGAACCAAGAAGGACAGAACAAATATATTCACAGAAACAGAA
GGGTTCAATGTCTGGAAGTCAATACAACATCAACTTCCAGCAAGGAGTTGCTGAGTCATTACATTCAGGATTACATCACA
GGTCTGACAAACTGATCATTCTTCAGTTAAACAAGAATATATTCACAAGGCAGGAAGCAGCAAACGCCATGGGCCAGTTT
CTTCTGCTTCTGTAATAGTTCCTCAGAAAATGTCATTAGATAAATAGAGAGGGAAATGAAAGCTAGAACCACTTGAACTG
GATGTAGGGGAACATTATGTAGCTGCCCAAACAGAGAAGCCCCACAAAAAACACATGAATTGCAGGCAGCCAACAGCAGT
TCTGTAACTTCTCTTATTAAAATGAAAATTCCTATTGCGAATGCAGAGAAACCAGAAAAAATACATTTTGGATAAAAAAG
TAAAAGAGTGGATCACTTAAACTGCGAACTCCAATTCCCCCCCCCCCCACTGATAAAAGTTCTAGTAAAGAAGAACTGAA
AATGAAAATAAATTTTCTTCTTTGGAAAGGCACAGTTCTTCTGATGGGGGCAGTGGAAAGAGCAAGCATTCAAGCCCACA
TGTGAGTAAAGACCACAAAGAAAAGTACAAGGAATATTCCTCCAACCACCATCACAGTAGCAGACACAAACATTCCCATT
CACATAGTGGCAGCAGTACTAGTGGCAATAAGCATAGTACTGATGGAATATCATCCACGGTTCTGAGGATTCCTGTTGGC
CTGAGTAGTGATGGTGGCAATTCCTCTAGTTCCAGTGCTACAAGAAAGAAGTTGCACATCAATGTTGCATCTCACAACTA
CCACTCCAAAATGAGTGAAAGTTCCAAAAGTTCAGGTGGACTACTGACATCT

ORF - retro_mdom_1109 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.5 %
Parental protein coverage: 64.03 %
Number of stop codons detected: 5
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPSVTLELLDELTHEFLQILEKTPNRLK
LT.FCLQYKPTV.AC.CIHL.CKWSNWEIPVSTD.KHW.EYV.PSVTLELLDELTH.FLQIL.KTPNRLK
RetrocopyLTAFCLQYKPTVTACLCIHLSCKWSNWEIPVSTD*KHWCEYVNPSVTLELLDELTHKFLQIL*KTPNRLK
ParentalRIRNWRATQAARKPKGDGQVSETALLGSSLVQNSILVDSVTGVTTNASFQKPSTSAFPAPVPLNSGNISV
RI...RA.Q.ARK.KGDGQVS.TALLGSSL.QNSILV.SVT.VT.NASFQKPS.SAFPAPVPLNSGNISV
RetrocopyRIWK*RANQVARKSKGDGQVSKTALLGSSLAQNSILVASVTHVTANASFQKPSISAFPAPVPLNSGNISV
ParentalQDTHASDNLTILTTGMPSTSYSLASHQEWPQHQEPTRTEQIYSQKQEAPMSGSQYNINFQQGPAGPLHSG
QD.H.SDNL.IL.TGM.STSYSL.SHQEWPQHQEP.RTEQIYSQKQ...MSGSQYNINFQQG.A..LHSG
RetrocopyQDSHTSDNLAILMTGMQSTSYSLGSHQEWPQHQEPRRTEQIYSQKQKGSMSGSQYNINFQQGVAESLHSG
ParentalLHHRSDKLSDHSSVKQEYTHK-AGSSKHHGPVSAAPVIVPQKMSLDKYREKRKLETLELDVREHYVAAQT
LHHRSDKL......K...T.....S..H.GPVS.A.VIVPQKMSLDK.R.K.KLE.LELDV.EHYVAAQT
RetrocopyLHHRSDKLIILQLNKNIFTRQ<GSSKRH-GPVSSASVIVPQKMSLDK*RGK*KLEPLELDVGEHYVAAQT
ParentalEQPHKKHM-QLQAASSSSVTSPIKMKIPIANAEKPE-KYMLDKKE-KSGSLKLRIPI--PPTDKSSSKEE
E.PHKKHM..LQAA.SSSVTS.IKMKIPIANAEKPE.KY.LDKK..KSGSLKLR.PI....TDKSSSKEE
RetrocopyEKPHKKHM<ELQAANSSSVTSLIKMKIPIANAEKPE>KYILDKKV>KSGSLKLRTPIXXXXTDKSSSKEE
ParentalLKMKI-KVSSSERHSSSDEGSGKSKHSSPHVSKDHKEKHKEHSSNRHHSSSHKHSHSHSGSSSSGSKHST
LKMKI.K.SS.ERHSSSD.GSGKSKHSSPHVSKDHKEK.KE.SSN.HHSS.HKHSHSHSGSS.SG.KHST
RetrocopyLKMKI<KFSSLERHSSSDGGSGKSKHSSPHVSKDHKEKYKEYSSNHHHSSRHKHSHSHSGSSTSGNKHST
ParentalDGIPPTVLRSPVGLSSDGGNSSSSSAARKKLHINDASHNHHSKMSKSSKSSGSSSSS
DGI..TVLR.PVGLSSDGGNSSSSSA.RKKLHIN.ASHN.HSKMS.SSKSSG....S
RetrocopyDGISSTVLRIPVGLSSDGGNSSSSSATRKKLHINVASHNYHSKMSESSKSSGGLLTS

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_1109 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1109 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 2 retrocopies.

Species Parental gene accession Retrocopies number
Monodelphis domestica ENSMODG00000000727 2 retrocopies
retro_mdom_1109 , retro_mdom_864,


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