RetrogeneDB ID:

retro_mdom_688

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:2:102482179..102482692(+)
Located in intron of:ENSMODG00000009507
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ASF1B
Ensembl ID:ENSMODG00000012099
Aliases:None
Description:anti-silencing function 1B histone chaperone [Source:HGNC Symbol;Acc:20996]


Retrocopy-Parental alignment summary:






>retro_mdom_688
AGCGAGGCCTTGGTCGACGCCCTAGAATGGAAAATAATTTATGTGGGTTCAGCAGAGAATGAGGAGTTTGACCAGATACT
AGACTCAGTGCTAGTAGGGCTAGTCCCAGCAGGGAGACACATGTTTGTCTTTCAGGCAGATGTCCCTAACACTTCCCTAA
ACCCAGAAACTGATTCAGTGGGTGTAACTGTGGTCCTCATAACTGGTACCTACCATGGGCAGGAGTTCATCCCAGTTGGG
TACTATGTCAACAATGAATATACCAACCCTGACTTCAGGAGAACCCAACCCTGAAACCAGATTTCTCTGAGCCCCATTGA
AACATGACTTCTAATCCCTGGGTGACTCGATTCCATATCAACTGGGACAGTACCACAGATAAATTGGAGGACATTGAAAA
CCAAGATCCTGTCTTAAGCCTGGGGCTCCCTTTGAATTGTCCCCCAACAATAAGGGCTAGATTTTCCAGACTGTGCCCCC
AGCATCATTCCTGAAAATTCCATGGGCTGCATC

ORF - retro_mdom_688 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.48 %
Parental protein coverage: 85.15 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalSEALADDLEWKIIYVGSAESEEFDQILDSVLVGPVPAGRHMFVFQADAPNASLIPETDAVGVTVVLITCT
SEAL.D.LEWKIIYVGSAE.EEFDQILDSVLVG.VPAGRHMFVFQAD.PN.SL.PETD.VGVTVVLIT.T
RetrocopySEALVDALEWKIIYVGSAENEEFDQILDSVLVGLVPAGRHMFVFQADVPNTSLNPETDSVGVTVVLITGT
ParentalYHGQEFIRVGYYVNNEYTNPE-LRENPPLKPDFSQLQRNILASNPRVTRFHINWDSTTDKLEDIENQDPV
YHGQEFI.VGYYVNNEYTNP..L.ENP.LKPDFS....N...SNP.VTRFHINWDSTTDKLEDIENQDPV
RetrocopyYHGQEFIPVGYYVNNEYTNPD<LQENPTLKPDFSEPH*N-MTSNPWVTRFHINWDSTTDKLEDIENQDPV
ParentalLSLGLPLSCPPTK-GLDLPDCAPSIIPENSMDCI
LSLGLPL.CPPT..GLD.PDCAPSIIPENSM.CI
RetrocopyLSLGLPLNCPPTI>GLDFPDCAPSIIPENSMGCI

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_688 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_688 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 6 parental genes, and 12 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000040851 retrocopy
Canis familiaris ENSCAFG000000164821 retrocopy
Echinops telfairi ENSETEG000000137131 retrocopy
Myotis lucifugus ENSMLUG000000005374 retrocopies
Monodelphis domestica ENSMODG00000012099 4 retrocopies
Sorex araneus ENSSARG000000005341 retrocopy



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