RetrogeneDB ID:

retro_mmus_402

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:1:185497369..185498014(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Nsa2
Ensembl ID:ENSMUSG00000060739
Aliases:Nsa2, 5730427N09Rik, LNR42, Nsa2p, Tinp1, Yr29
Description:NSA2 ribosome biogenesis homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1913883]


Retrocopy-Parental alignment summary:






>retro_mmus_402
TTAGTATCATTTGGGACTAAGCTTTACCATAAATAGTGCCATGCTGAGAAAATACAGATGAAAAAGACTATTAAGATGCA
TGAAAAGAGAAACCGCAAGCAAAAGCACGACGGGAAGACGCCACAGGGAGCAGTTCCTGCCTGTCTGCTGGACAGAGAGG
GGCAGTCGAGGGCAAAATTACTTTCCAACATGATTAAGCAGAAACAAGAAGAGAAGGCAGGAAAATGGGAAGTTCCTCTA
CCCAAAGTTCGTGGCCAAGGAGAATCAGAAGTATTGAAAGTTATTCAAACAGGAAAGAAAAAAAACGAAGGCAGGGAAGA
GAATGGTTACTAACGCGTGCTCTGTTGGTGATGGTTTGACATAAAATGCATCTAAATATGAAAGGTTCATTAGGCCACTG
GGCCCATGCTTCCAAAAGCCCATGTCACACACCCTGAGCTGAAAGCCACCTTTAGCCTGTCAATATGTGGTGTGAACAAG
AATCCATCATCCCCATTGTATTCAAATCTGGTGTGATCACCAAAGGTGCAGTTACTGAGAGAATGTGAGCGAGCCAGGCC
TTGTGACACAGGAGGGAGGGTGATTTGGGGTGAGTGTGCCCAAGTTACTGAAAACAACAGGTGCATAAGTGAGGTCTTGC
TGATC

ORF - retro_mmus_402 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.21 %
Parental protein coverage: 84.23 %
Number of stop codons detected: 2
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalMIGLKAKLYHKQRHAEKIQMKKTIKMHEKRNTKQKDDEKTPQGAVPAYLLDREGQSRAKVLSNMIKQKRK
......KLYHK..HAEKIQMKKTIKMHEKRN.KQK.D.KTPQGAVPA.LLDREGQSRAK.LSNMIKQK..
RetrocopyLVSFGTKLYHK*CHAEKIQMKKTIKMHEKRNRKQKHDGKTPQGAVPACLLDREGQSRAKLLSNMIKQKQE
ParentalEKAGKWEVPLPKVRAQGETEVLKVIRTGK-RKKKAWKRMVTKVCFVGDGFTRKPPKYERFIRPMGLRFK-
EKAGKWEVPLPKVR.QGE.EVLKVI.TGK....KA.KRMVT..C.VGDG.T....KYERFIRP.G..F..
RetrocopyEKAGKWEVPLPKVRGQGESEVLKVIQTGK>XXXKAGKRMVTNACSVGDGLT*NASKYERFIRPLGPCFQ<
ParentalKAHVTHPELKATFCLPILGVKKNPSSPLYTTL-GVITKGTVIE-VNVSELGLVTQ-GGKVIWGKYAQVTN
KAHVTHPELKATF.L.I.GV.KNPSSPLY..L.GVITKG.V.E..NVSE.GLVTQ.GG.VIWG..AQVT.
RetrocopyKAHVTHPELKATFSLSICGVNKNPSSPLYSNL<GVITKGAVTE<ENVSEPGLVTQ<GGRVIWGECAQVT-
ParentalNPENDGCINAVLLV
..EN..CI..VLL.
Retrocopy--ENNRCISEVLLI

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 .30 RPM 10 .05 RPM
SRP007412_cerebellum 0 .17 RPM 9 .99 RPM
SRP007412_heart 0 .00 RPM 16 .09 RPM
SRP007412_kidney 0 .00 RPM 22 .87 RPM
SRP007412_liver 0 .00 RPM 19 .72 RPM
SRP007412_testis 0 .00 RPM 25 .52 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_402 was not detected
No EST(s) were mapped for retro_mmus_402 retrocopy.
No TSS is located nearby retro_mmus_402 retrocopy 5' end.
retro_mmus_402 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_402 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Rattus norvegicus retro_rnor_945

Parental genes homology:
Parental genes homology involve 17 parental genes, and 148 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000030663 retrocopies
Canis familiaris ENSCAFG000000083114 retrocopies
Callithrix jacchus ENSCJAG000000168741 retrocopy
Equus caballus ENSECAG000000055281 retrocopy
Echinops telfairi ENSETEG0000000409513 retrocopies
Felis catus ENSFCAG000000119781 retrocopy
Loxodonta africana ENSLAFG000000099104 retrocopies
Macropus eugenii ENSMEUG000000157983 retrocopies
Myotis lucifugus ENSMLUG000000144644 retrocopies
Monodelphis domestica ENSMODG000000019004 retrocopies
Mus musculus ENSMUSG00000060739 25 retrocopies
Oryctolagus cuniculus ENSOCUG000000065366 retrocopies
Pteropus vampyrus ENSPVAG000000053962 retrocopies
Rattus norvegicus ENSRNOG0000001653015 retrocopies
Sorex araneus ENSSARG000000094244 retrocopies
Sus scrofa ENSSSCG000000140752 retrocopies
Tupaia belangeri ENSTBEG0000001297856 retrocopies



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