RetrogeneDB ID:

retro_mdom_1925

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:8:175472347..175473063(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:WWTR1
Ensembl ID:ENSMODG00000021266
Aliases:None
Description:WW domain containing transcription regulator 1 [Source:HGNC Symbol;Acc:24042]


Retrocopy-Parental alignment summary:






>retro_mdom_1925
GAGATGACTTTCACTGCCACTGGCCAGCGGTATTTTCTCAATCACATAGAAAAAATCACCTCATGGCAAGACCCTCAGAA
GACAATAACTCAAACTTTGAACCACATGGCTTTCCATCCCTCGGCAACTTCAACCCCAATGTCCTAGATTCCATGGTGAT
GTCTCAGCCCAACCTTGTGATGAACCACCAGCACCAGCAGCAGATAACATCCAATATCACTCTGTCCCAGCAAAACCATC
CAGCCCCAAACCCACAGGATGGCTTGATGAGTTTGCCCAAAGCCTTGACCACCCAGCAGTAACCTCAACAGAAACTATGG
CTTCAGCAGATCCAAATGGAAAGAGAAAGAATCCAAATGTGCCAGTAGGAACTCATTAGACAGGAAGCTATTTTGTGTCA
ACAACTTCCCATGGAATCAGAGAAAATGGCCTCTGTTCAACCTGCTGGGAATACACCTGCCATAGCCCAGGAACTAAGAC
CAATAACAAATAATAGTTCGGATCCATTTCTCAATGGCGGGCCAAACCATTCTAGGGAACAGAGCACTGACAGTGGCCTT
GTCTTAGGATGCTACAGCATACAAACGACTCCTAAAGATTTCCTTGGCAACATTGATGAGATGGACACAGGGGAAACTGT
AGCCAATACACCGATGAACCTAAATGTCCAGCAGATCCATTTCCCTGACTTCCTTGACTATCTTCCTGCAACAGAC

ORF - retro_mdom_1925 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.5 %
Parental protein coverage: 57.87 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalEMTFTATGQRYFLNHIEKITTWQDPRKTMTQPLNHMALHPSATSTPMP-QRSMAMSQPNLVMNHQHQQQM
EMTFTATGQRYFLNHIEKIT.WQDP.KT.TQ.LNHMA.HPSATSTPM....SM.MSQPNLVMNHQHQQQ.
RetrocopyEMTFTATGQRYFLNHIEKITSWQDPQKTITQTLNHMAFHPSATSTPMS<LDSMVMSQPNLVMNHQHQQQI
ParentalTSNTTLSQQNHPAPNPQAGLMSLPNALTTQQQQQQKLRLQRIQMERERIRMRQEELMRQEAALCRQLPME
TSN.TLSQQNHPAPNPQ.GLMSLP.ALTTQQ..QQKL.LQ.IQMERERI.M.Q.EL.RQEA.LC.QLPME
RetrocopyTSNITLSQQNHPAPNPQDGLMSLPKALTTQQ*PQQKLWLQQIQMERERIQMCQ*ELIRQEAILCQQLPME
ParentalSETMASVQATGNTPAMAQEIRPITNNSSDPFLNGGPYHSREQSTDSGLGLGCYSIPTTPEDFLGNVDEMD
SE.MASVQ..GNTPA.AQE.RPITNNSSDPFLNGGP.HSREQSTDSGL.LGCYSI.TTP.DFLGN.DEMD
RetrocopySEKMASVQPAGNTPAIAQELRPITNNSSDPFLNGGPNHSREQSTDSGLVLGCYSIQTTPKDFLGNIDEMD
ParentalTGENVAQTPMNLNAQQTRFPDFLDCLPGTN
TGE.VA.TPMNLN.QQ..FPDFLD.LP.T.
RetrocopyTGETVANTPMNLNVQQIHFPDFLDYLPATD

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_1925 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1925 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 ENSMODG00000021266 1 retrocopy
retro_mdom_1925 ,


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