RetrogeneDB ID:

retro_mdom_694

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:2:130292748..130293246(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS3A
Ensembl ID:ENSMODG00000000969
Aliases:None
Description:ribosomal protein S3A [Source:HGNC Symbol;Acc:10421]


Retrocopy-Parental alignment summary:






>retro_mdom_694
AAGAATGAAAAGGATGCTTTAAATAAGTTCAAGTCAATTTCTTTATATTTTCAGGGTAAAAATTATTTGACAATTTCCAT
GGAATGGACCTTACCTTTGATAAGGATTGATCCATGGTCAAAAAATGGCAAATTACAACTGAATTCCATATTTATGTAAA
AAGTACTAATGCTTATTTGATCTGCCTTTTCAATATTCGTTTTACTAAGAAGCTCAACAAACAGGTCCGTAAGTTCTTTC
ATGAACAGTACCAAGAGGTCCATCAAATTTGCATGAAGATGATGAAAATCAAGTCAGGGAATATAGACAAATGACTTGAA
AGAATTTGTCAATAAATTGATTCCAGGCCACAATGGAAAAAGATATAGAAAAGATTTGTCAGTCCATTTACTCTTTTTGA
GATGTATTTGTTTGAAAAGAAAAAAGATGCTCAAGAAGCCCAAATTTGAACTTAGAAAACTATTGGAATTACAGGATAAT
TATGGAGGTTTTCAGAAA

ORF - retro_mdom_694 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 55.23 %
Parental protein coverage: 62.88 %
Number of stop codons detected: 3
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalQNDEVAFRKFKLITEDVQGKNCLT-NFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCVGFT
.N...A..KFK.I....QGKN.LT.NFHGMDLT.DK..SMVKKWQ...E.H..VK.T..YL..LF...FT
RetrocopyKNEKDALNKFKSISLYFQGKNYLT<NFHGMDLTFDKD*SMVKKWQITTEFHIYVKSTNAYLICLFNIRFT
ParentalKKRNNQIRKTSYAQHQQVRQIRKKMMEIMT-REVQ-TNDLKEVVNKLIPDSIG-KDIEKACQSIYPLHDV
KK.N.Q.RK....Q.Q.V.QI..KMM.I...RE...TNDLKE.VNKLIP...G.KDIEK.CQSIY...DV
RetrocopyKKLNKQVRKFFHEQYQEVHQICMKMMKIKS<REYR<TNDLKEFVNKLIPGHNG>KDIEKICQSIYSF*DV
ParentalFVRKVKML-KKPKFEL-GKLMELHGEGGGSGK
FV.K.K.....P...L..KL.EL....GG..K
RetrocopyFV*KEKRCSRSPNLNL<RKLLELQDNYGGFQK

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_694 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_694 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 32 parental genes, and 397 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001842511 retrocopies
Bos taurus ENSBTAG000000099083 retrocopies
Canis familiaris ENSCAFG000000079907 retrocopies
Choloepus hoffmanni ENSCHOG0000000723834 retrocopies
Callithrix jacchus ENSCJAG000000022687 retrocopies
Cavia porcellus ENSCPOG000000155699 retrocopies
Dipodomys ordii ENSDORG0000000225010 retrocopies
Equus caballus ENSECAG000000095736 retrocopies
Erinaceus europaeus ENSEEUG000000049944 retrocopies
Felis catus ENSFCAG000000312885 retrocopies
Homo sapiens ENSG0000014542540 retrocopies
Gorilla gorilla ENSGGOG000000031822 retrocopies
Loxodonta africana ENSLAFG000000176603 retrocopies
Microcebus murinus ENSMICG000000049219 retrocopies
Myotis lucifugus ENSMLUG000000147888 retrocopies
Macaca mulatta ENSMMUG000000218211 retrocopy
Monodelphis domestica ENSMODG00000000969 6 retrocopies
Mustela putorius furoENSMPUG000000071398 retrocopies
Mus musculus ENSMUSG000000280812 retrocopies
Nomascus leucogenys ENSNLEG0000000581526 retrocopies
Oryctolagus cuniculus ENSOCUG000000070111 retrocopy
Procavia capensis ENSPCAG000000150406 retrocopies
Pongo abelii ENSPPYG0000002586927 retrocopies
Pteropus vampyrus ENSPVAG0000001540624 retrocopies
Rattus norvegicus ENSRNOG000000118931 retrocopy
Sorex araneus ENSSARG0000000071715 retrocopies
Sarcophilus harrisii ENSSHAG000000150882 retrocopies
Sus scrofa ENSSSCG000000090193 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000242031 retrocopy
Tupaia belangeri ENSTBEG0000000296398 retrocopies
retro_tbel_1005, retro_tbel_11, retro_tbel_1119, retro_tbel_116, retro_tbel_1232, retro_tbel_1318, retro_tbel_133, retro_tbel_137, retro_tbel_1375, retro_tbel_1378, retro_tbel_1383, retro_tbel_1417, retro_tbel_1421, retro_tbel_1509, retro_tbel_1686, retro_tbel_1698, retro_tbel_172, retro_tbel_1720, retro_tbel_1721, retro_tbel_1744, retro_tbel_1814, retro_tbel_1829, retro_tbel_1856, retro_tbel_1896, retro_tbel_1948, retro_tbel_1960, retro_tbel_1999, retro_tbel_206, retro_tbel_2200, retro_tbel_2306, retro_tbel_2463, retro_tbel_2483, retro_tbel_2510, retro_tbel_2626, retro_tbel_2654, retro_tbel_2657, retro_tbel_2745, retro_tbel_2759, retro_tbel_2760, retro_tbel_2764, retro_tbel_281, retro_tbel_2857, retro_tbel_2957, retro_tbel_2959, retro_tbel_3114, retro_tbel_317, retro_tbel_3212, retro_tbel_3255, retro_tbel_3259, retro_tbel_3299, retro_tbel_336, retro_tbel_3372, retro_tbel_3416, retro_tbel_3471, retro_tbel_3486, retro_tbel_3513, retro_tbel_3558, retro_tbel_3613, retro_tbel_3631, retro_tbel_3655, retro_tbel_3705, retro_tbel_373, retro_tbel_375, retro_tbel_3755, retro_tbel_3786, retro_tbel_3815, retro_tbel_3823, retro_tbel_3832, retro_tbel_386, retro_tbel_3882, retro_tbel_39, retro_tbel_3947, retro_tbel_3966, retro_tbel_399, retro_tbel_4116, retro_tbel_4144, retro_tbel_4147, retro_tbel_4211, retro_tbel_4220, retro_tbel_423, retro_tbel_4294, retro_tbel_4304, retro_tbel_4347, retro_tbel_438, retro_tbel_4428, retro_tbel_445, retro_tbel_4579, retro_tbel_598, retro_tbel_619, retro_tbel_623, retro_tbel_671, retro_tbel_859, retro_tbel_90, retro_tbel_912, retro_tbel_92, retro_tbel_928, retro_tbel_956, retro_tbel_973,
Tursiops truncatus ENSTTRG0000001309410 retrocopies
Vicugna pacos ENSVPAG000000042358 retrocopies



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