RetrogeneDB ID:

retro_mdom_617

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:1:549533857..549535022(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CNOT2
Ensembl ID:ENSMODG00000020387
Aliases:None
Description:CCR4-NOT transcription complex, subunit 2 [Source:HGNC Symbol;Acc:7878]


Retrocopy-Parental alignment summary:






>retro_mdom_617
ATTCTTACCCTCCCTGCCCAAACTGCAACCCAAACAACAAGCCAAACAGCAGTAATCACAGACAGTTCAATTAAATGCCT
TCCAATGAGGGGAATGAGAAACAATACCCCTCAGTTAAATCACAGCTTATCCCAAGACACTCAGTAACCAAGCCACGTCA
CACCAACAACAGAGGTACCAACAATATCACTTCATATGCTTCCATCTCCAAGCAACCTATGAATCCTAGGAATATGATGA
ACCACTCCCAAGTTTGTCAGGACATTGGAATTGCCAAAAGGACAAATAGCATGAGCAGTTCAGGATTAGGTAACCCTAAC
AGAATTTCACCAAGCATAATATGTATACCAAAGCAGCAACCCTCTAGACAACCTTTTACTGTGAATTGTAGGTCTGGATT
TGGAATGAACAAGAATCAGGCATTCGGAATAAATAATTCTCTATCAAGTAACATTTTAATGGAACAGATGGAAGTGAAAA
TGTGACAGGACTGGACCTTTCAGATTTTCCAGCACTAGCAGATCTAAACAGAAGGGAAGGAAACAGTAACCCAACTCCAT
TAATAAACCCCTTATCTGGAAGAGCTCCTTATGTTGGAATGGTAACAAAACCAGCAAGTGAGCAATCCCAAGATTTCTCA
ATACACAATGAAGATTTTCCAGTATTGTCAGGCTCCAGTTATAAAGATCCAATAACAAATAATGAGGATAGCAAATCTAA
TTTTAATACATCTGGTGAGACATCTTCAAGTACAGATGGACCTAAATTTCCTGGAGACAAAAGTTCAACAGCAAAAATCA
ACAACCAGCAGAAAAAAGGGATCCAGGTATTACCTGATGGTCAAATTACTAACATTCCTCAAGGGATGGTGATGGACCAA
TTTGGAATGATTGGCCTGCTGACATTCATTAGAGCAGCAGAGATAGACCCAGAAATTGTACAGCTTGCATTAAGAAGTCA
CTTAAGAACACTAAGCCTCAATCTCAAATTCCCTGAAAATCTCTATCCCAAATTTGCATCACCTTGGGTGTCTTCATCTT
GTTGACCTGAAGACATAGACTTCCATTTTCCAACTGAATACTTAAGGAACAGTCACATTAGAGATAAGCTGGCTGCAATA
AAATTGGGCTGATATGGAGATCTACTATTCTATTTCTATTACATA

ORF - retro_mdom_617 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.96 %
Parental protein coverage: 70.56 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMLASPSTSGQLSQFGASLYGQQSALGLPMRGMSNNTPQLNRSLSQGTQLPSHVTPTTGVPTMSLHTPPSP
.L..P.................S...LPMRGM.NNTPQLN.SLSQ.TQ.PSHVTPTT.VPT.SLH..PSP
RetrocopyILTLPAQTATQTTSQTAVITDSSIKCLPMRGMRNNTPQLNHSLSQDTQ*PSHVTPTTEVPTISLHMLPSP
ParentalS-RGILPMNPRNMMNHSQVGQGIGIASRTNSMSSSGLGSPNRSSPSIICMPKQQPSRQPFTVNSMSGFGM
S.....P.N..N...HSQV.Q.IGIA.RTNSMSSSGLG.PNR.SPSIIC.PKQQPSRQPFTVN..SGFGM
RetrocopyS<QPMNPRNMMN---HSQVCQDIGIAKRTNSMSSSGLGNPNRISPSIICIPKQQPSRQPFTVNCRSGFGM
ParentalNRNQAFGMNNSLSSNI-FNGTDGSENVTGLDLSDFPALADRNRREGSGNPTPLINPLAGRAPYVGMVTKP
N.NQAFG.NNSLSSNI.FNGTDGSENVTGLDLSDFPALAD.NRREG..NPTPLINPL.GRAPYVGMVTKP
RetrocopyNKNQAFGINNSLSSNI<FNGTDGSENVTGLDLSDFPALADLNRREGNSNPTPLINPLSGRAPYVGMVTKP
ParentalASEQSQDFSIHNEDFPALPGSSYKDPTTSNEDSKSNLNTSGKTSSSTDGPKFPGDKSSTTQNNNQQKKGI
ASEQSQDFSIHNEDFP.L.GSSYKDP.T.NEDSKSN.NTSG.TSSSTDGPKFPGDKSST...NNQQKKGI
RetrocopyASEQSQDFSIHNEDFPVLSGSSYKDPITNNEDSKSNFNTSGETSSSTDGPKFPGDKSSTAKINNQQKKGI
ParentalQVLPDGRVTNIPQGMVTDQFGMIGLLTFIRAAETDPGMVHLALGSDLTTLGLNLNSPENLYPKFASPWAS
QVLPDG..TNIPQGMV.DQFGMIGLLTFIRAAE.DP..V.LAL.S.L.TL.LNL..PENLYPKFASPW.S
RetrocopyQVLPDGQITNIPQGMVMDQFGMIGLLTFIRAAEIDPEIVQLALRSHLRTLSLNLKFPENLYPKFASPWVS
ParentalSPCRPQDIDFHVPSEYLTNIHIRDKLAAIKLGRYGEDLLFYLYYM
S.C.P.DIDFH.P.EYL.N.HIRDKLAAIKLG.YG.DLLFY.YY.
RetrocopySSC*PEDIDFHFPTEYLRNSHIRDKLAAIKLG*YG-DLLFYFYYI

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 2 .15 RPM 0 .00 RPM
SRP007412_cerebellum 0 .33 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_617 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_617 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 ENSMODG00000020387 1 retrocopy
retro_mdom_617 ,


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