RetrogeneDB ID:

retro_mdom_1267

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:4:176786080..176786439(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS25
Ensembl ID:ENSMODG00000013334
Aliases:None
Description:ribosomal protein S25 [Source:HGNC Symbol;Acc:10413]


Retrocopy-Parental alignment summary:






>retro_mdom_1267
AAGGATAACAACAAGAAGAAGGATGCTGGCAAGTCATACTAAAAGAATAAAGACCCCACGAATAGGTCTGGAGGCACAAT
TAAGAAGAAATGATCCAAAGGAAAAGTCCAAGACAAGTTCAACATTTTGGTTCTTTTTGACAAAGCAATATATGACAAAC
TCTGCAAAGAGGTCCTCAACTGAAACTTCTCACCCCTTCAATAGTCTCAGAGAGATTGAAGATCTATGGCTCGCTAGCCC
TGGCAGCTCTTCAGGAACTGCTTAGTAAAGATATAATGAAGTTAGTTTCTAGACACAAAGCACAAGTAATATATACTAGG
AACACCAAAGGTGGAGAGGTTTCAGCTACTGAAGATGCA

ORF - retro_mdom_1267 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.54 %
Parental protein coverage: 97.6 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalKDDKKKKDAGKSAKKDKDPVNKSGGKAKKKVKAIWGKVRDKLNNLVLFDKATYDKLCKEV-PNYKLITPA
KD..KKKDAGKS..K.KDP.N.SGG..KKK.....GKV.DK.N.LVLFDKA.YDKLCKEV.P..KL.TP.
RetrocopyKDNNKKKDAGKSY*KNKDPTNRSGGTIKKK*SK--GKVQDKFNILVLFDKAIYDKLCKEV<PQLKLLTPS
ParentalVVSERLKIRGSLARAALQELLSKGLIKLVSKHRAQVIYTRNTKGGDAPAAEDA
.VSERLKI.GSLA.AALQELLSK...KLVS.H.AQVIYTRNTKGG...A.EDA
RetrocopyIVSERLKIYGSLALAALQELLSKDIMKLVSRHKAQVIYTRNTKGGEVSATEDA

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_1267 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1267 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 10 parental genes, and 60 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000000515 retrocopies
Canis familiaris ENSCAFG000000123953 retrocopies
Cavia porcellus ENSCPOG000000132982 retrocopies
Felis catus ENSFCAG000000011513 retrocopies
Loxodonta africana ENSLAFG000000171176 retrocopies
Microcebus murinus ENSMICG000000026878 retrocopies
Myotis lucifugus ENSMLUG0000000475215 retrocopies
Monodelphis domestica ENSMODG00000013334 2 retrocopies
retro_mdom_1267 , retro_mdom_1615,
Mustela putorius furoENSMPUG000000049604 retrocopies
Sus scrofa ENSSSCG0000001510312 retrocopies



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