RetrogeneDB ID:

retro_mdom_337

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:1:210691771..210692322(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000017548
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000003534
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_337
ATGGTGAGGTATTCTCTTGATCCAGAGAATCCTACAAAATCATGCAAGCCAAGGGGCTCAAATCTCCGGGTCCACTTCAA
GAACACCTATGAAACAGCCCAAGCTATCAAGGGCATGCATATCCAAAAAGCTACCAAATATTTGAAAGATGTCACATTGA
AGAAACAGTGTGTTCCTTTCCCTCGGTACAATGGTGGAGTTGGCAGGTGTGCCCAGGCTAAGCAATGGGGTTGGACACAA
GGTCGTTGGCCCAAAAAGAGTGCTGATTCTTGCTGCATATGCTTAAAAATGCAGAAAGTAATGCAGAACTTAAGGGTTTG
GATGTGGATTCTCTTGTCATTGAGCATATCCAGGTTAACAAAGCTCCCAAAATGCGAAGACAGACTTACAGAACTCATGG
GCGAATTAACCCATACATGAGTTCCCCTTGCCATATTGAGATGATACTTACTGAAAAGGAGCAGATTGTTCCTAAACTAG
AAGAAGAGGTTGCTCAAAAGAAAAAGATATCCCAAAAGAAACTGAAGAAACAAAAACTTATGGCATGGGAG

ORF - retro_mdom_337 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.03 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMVRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLKKQCVPFRRYNGGVGRC
MVRYSLDPENPTKSCK.RGSNLRVHFKNT.ETAQAIKGMHI.KATKYLKDVTLKKQCVPF.RYNGGVGRC
RetrocopyMVRYSLDPENPTKSCKPRGSNLRVHFKNTYETAQAIKGMHIQKATKYLKDVTLKKQCVPFPRYNGGVGRC
ParentalAQAKQWGWTQGRWPKKSAE-FLLHMLKNAESNAELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPY
AQAKQWGWTQGRWPKKSA..FLLHMLKNAESNAELKGLDVDSLVIEHIQVNKAPKMRR.TYR.HGRINPY
RetrocopyAQAKQWGWTQGRWPKKSAD<FLLHMLKNAESNAELKGLDVDSLVIEHIQVNKAPKMRRQTYRTHGRINPY
ParentalMSSPCHIEMILTEKEQIVPKPEEEVAQKKKISQKKLKKQKLMARE
MSSPCHIEMILTEKEQIVPK.EEEVA..............LMA.E
RetrocopyMSSPCHIEMILTEKEQIVPKLEEEVAXXXXXXXXXXXXXXLMAWE

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 .36 RPM 0 .00 RPM
SRP007412_cerebellum 0 .00 RPM 0 .00 RPM
SRP007412_heart 0 .20 RPM 0 .00 RPM
SRP007412_kidney 1 .32 RPM 0 .00 RPM
SRP007412_liver 1 .51 RPM 0 .00 RPM
SRP007412_testis 0 .39 RPM 0 .00 RPM
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_337 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_337 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 21 parental genes, and 478 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000229025 retrocopies
Choloepus hoffmanni ENSCHOG0000000787250 retrocopies
Echinops telfairi ENSETEG0000001132210 retrocopies
Homo sapiens ENSG000002154721 retrocopy
Latimeria chalumnae ENSLACG000000088351 retrocopy
Macropus eugenii ENSMEUG0000001670926 retrocopies
Microcebus murinus ENSMICG0000001710214 retrocopies
Myotis lucifugus ENSMLUG0000002555422 retrocopies
Myotis lucifugus ENSMLUG0000002926436 retrocopies
Macaca mulatta ENSMMUG0000001883726 retrocopies
Monodelphis domestica ENSMODG00000003534 11 retrocopies
Oryctolagus cuniculus ENSOCUG000000124852 retrocopies
Procavia capensis ENSPCAG000000031038 retrocopies
Pongo abelii ENSPPYG0000000915143 retrocopies
Pteropus vampyrus ENSPVAG0000000196976 retrocopies
Rattus norvegicus ENSRNOG0000001868048 retrocopies
Sarcophilus harrisii ENSSHAG0000000306014 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000000519333 retrocopies
Tarsius syrichta ENSTSYG0000000740220 retrocopies
Tursiops truncatus ENSTTRG0000000579731 retrocopies
Vicugna pacos ENSVPAG000000095681 retrocopy



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