RetrogeneDB ID:

retro_mmus_1123

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:13:78273471..78273952(-)
Located in intron of:ENSMUSG00000087143
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Rpl21
Ensembl ID:ENSMUSG00000041453
Aliases:Rpl21, 8430440E03Rik, L21
Description:ribosomal protein L21 [Source:MGI Symbol;Acc:MGI:1278340]


Retrocopy-Parental alignment summary:






>retro_mmus_1123
ATGACGAACACAAAGGGAAAGAGGAGAGGCACCCGGTGTATGTTCTCTAGGCCTTTTAGGAAACATGGCGTTGTTCCTTT
GGCCACATACATGTGAATCTACAAGAAGGGTGTTATTGTAGACATCAAGGGAATGGGCACTGTTCAAAAAAGGAATGCCC
CATAAGTGCTACCATGGCAAAACCAGAAGAGTCTACAATGTCACCCAGCATGACTTGGGCATCATTGTAAACAAGCAGGT
TAAGGGCAAAATTCTGGCCAAGAGGATCAATGTGCGGATTGAGCACAGCAAGCACTCAAAGAGCAGGAACAGCTTCCTAA
AGCTGGTGAAGGAGAACGACCAGAAGAAAAAGGAAGCCAAAGGGAAAGGCACCTGGGTGCAGCTGAAGCGCCAGCCTGCG
CCACTCAGAGAAGCACACTTTGTGAGGACTAACAGAAAAGAACCTGAGCTGTTGGAGCCCATTCCATACAAATTCATGGC
C

ORF - retro_mmus_1123 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.3 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMTNTKGKRRGTRYMFSRPFRKHGVVPLATYMRIYKKGDIVDIKGMGTVQK-GMPHKCYHGKTGRVYNVTQ
MTNTKGKRRGTR.MFSRPFRKHGVVPLATYM.IYKKG.IVDIKGMGTVQK.GMPHKCYHGKT.RVYNVTQ
RetrocopyMTNTKGKRRGTRCMFSRPFRKHGVVPLATYM*IYKKGVIVDIKGMGTVQK>GMPHKCYHGKTRRVYNVTQ
ParentalHAVGIIVNKQVKGKILAKRINVRIEHIKHSKSRDSFLKRVKENDQKKKEAKEKGTWVQLKRQPAPPREAH
H..GIIVNKQVKGKILAKRINVRIEH.KHSKSR.SFLK.VKENDQKKKEAK.KGTWVQLKRQPAP.REAH
RetrocopyHDLGIIVNKQVKGKILAKRINVRIEHSKHSKSRNSFLKLVKENDQKKKEAKGKGTWVQLKRQPAPLREAH
ParentalFVRTNGKEPELLEPIPYEFMA
FVRTN.KEPELLEPIPY.FMA
RetrocopyFVRTNRKEPELLEPIPYKFMA

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 .02 RPM 120 .25 RPM
SRP007412_cerebellum 0 .04 RPM 84 .19 RPM
SRP007412_heart 0 .03 RPM 113 .97 RPM
SRP007412_kidney 0 .04 RPM 114 .23 RPM
SRP007412_liver 0 .00 RPM 90 .42 RPM
SRP007412_testis 0 .00 RPM 66 .60 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_1123 was not detected
No EST(s) were mapped for retro_mmus_1123 retrocopy.
No TSS is located nearby retro_mmus_1123 retrocopy 5' end.
retro_mmus_1123 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_1123 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 31 parental genes, and 593 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000031691 retrocopy
Bos taurus ENSBTAG000000016485 retrocopies
Choloepus hoffmanni ENSCHOG000000078676 retrocopies
Callithrix jacchus ENSCJAG000000193551 retrocopy
Cavia porcellus ENSCPOG000000087843 retrocopies
Dipodomys ordii ENSDORG0000000222615 retrocopies
Equus caballus ENSECAG000000106615 retrocopies
Felis catus ENSFCAG000000067501 retrocopy
Homo sapiens ENSG00000122026105 retrocopies
retro_hsap_1007, retro_hsap_1011, retro_hsap_1019, retro_hsap_1032, retro_hsap_1040, retro_hsap_1099, retro_hsap_1107, retro_hsap_1213, retro_hsap_1218, retro_hsap_122, retro_hsap_1280, retro_hsap_1288, retro_hsap_1298, retro_hsap_1379, retro_hsap_1381, retro_hsap_1419, retro_hsap_143, retro_hsap_1430, retro_hsap_1446, retro_hsap_1453, retro_hsap_1505, retro_hsap_1576, retro_hsap_1578, retro_hsap_160, retro_hsap_1600, retro_hsap_1663, retro_hsap_1712, retro_hsap_1723, retro_hsap_1734, retro_hsap_1757, retro_hsap_1805, retro_hsap_1842, retro_hsap_1886, retro_hsap_1904, retro_hsap_1920, retro_hsap_2050, retro_hsap_2088, retro_hsap_2109, retro_hsap_2153, retro_hsap_2178, retro_hsap_2221, retro_hsap_2245, retro_hsap_2258, retro_hsap_2266, retro_hsap_2357, retro_hsap_2442, retro_hsap_252, retro_hsap_2625, retro_hsap_2635, retro_hsap_2655, retro_hsap_2716, retro_hsap_2855, retro_hsap_2876, retro_hsap_2916, retro_hsap_2937, retro_hsap_3037, retro_hsap_3039, retro_hsap_3091, retro_hsap_3094, retro_hsap_3119, retro_hsap_3160, retro_hsap_3185, retro_hsap_3264, retro_hsap_3304, retro_hsap_3375, retro_hsap_3429, retro_hsap_3435, retro_hsap_3521, retro_hsap_3555, retro_hsap_3558, retro_hsap_362, retro_hsap_3628, retro_hsap_3658, retro_hsap_3662, retro_hsap_367, retro_hsap_3688, retro_hsap_3694, retro_hsap_3705, retro_hsap_3747, retro_hsap_3764, retro_hsap_381, retro_hsap_3911, retro_hsap_3945, retro_hsap_3955, retro_hsap_4092, retro_hsap_4193, retro_hsap_424, retro_hsap_4276, retro_hsap_4283, retro_hsap_4286, retro_hsap_4302, retro_hsap_4713, retro_hsap_4733, retro_hsap_496, retro_hsap_503, retro_hsap_563, retro_hsap_573, retro_hsap_582, retro_hsap_626, retro_hsap_654, retro_hsap_738, retro_hsap_752, retro_hsap_819, retro_hsap_900, retro_hsap_965,
Latimeria chalumnae ENSLACG000000126781 retrocopy
Loxodonta africana ENSLAFG0000000367711 retrocopies
Microcebus murinus ENSMICG0000001475454 retrocopies
Myotis lucifugus ENSMLUG0000001009346 retrocopies
Macaca mulatta ENSMMUG000000233682 retrocopies
Macaca mulatta ENSMMUG000000295742 retrocopies
Monodelphis domestica ENSMODG000000089231 retrocopy
Mustela putorius furoENSMPUG0000000935323 retrocopies
Mus musculus ENSMUSG00000041453 101 retrocopies
retro_mmus_1012, retro_mmus_1046, retro_mmus_1057, retro_mmus_1083, retro_mmus_1123 , retro_mmus_1199, retro_mmus_1287, retro_mmus_1354, retro_mmus_1461, retro_mmus_1475, retro_mmus_1529, retro_mmus_1561, retro_mmus_1572, retro_mmus_1596, retro_mmus_1617, retro_mmus_1641, retro_mmus_1644, retro_mmus_17, retro_mmus_1714, retro_mmus_1739, retro_mmus_1762, retro_mmus_1797, retro_mmus_1848, retro_mmus_1860, retro_mmus_1862, retro_mmus_1875, retro_mmus_1897, retro_mmus_1915, retro_mmus_1931, retro_mmus_1936, retro_mmus_1994, retro_mmus_2042, retro_mmus_2049, retro_mmus_2101, retro_mmus_2130, retro_mmus_2176, retro_mmus_2179, retro_mmus_2185, retro_mmus_2214, retro_mmus_2233, retro_mmus_2237, retro_mmus_2238, retro_mmus_2279, retro_mmus_2309, retro_mmus_2312, retro_mmus_2335, retro_mmus_2344, retro_mmus_2395, retro_mmus_2447, retro_mmus_2517, retro_mmus_2567, retro_mmus_2585, retro_mmus_2598, retro_mmus_266, retro_mmus_2662, retro_mmus_2698, retro_mmus_2707, retro_mmus_2778, retro_mmus_2808, retro_mmus_2853, retro_mmus_2874, retro_mmus_2945, retro_mmus_2980, retro_mmus_3035, retro_mmus_3055, retro_mmus_3085, retro_mmus_3103, retro_mmus_3112, retro_mmus_3220, retro_mmus_3252, retro_mmus_3261, retro_mmus_3295, retro_mmus_3318, retro_mmus_3328, retro_mmus_333, retro_mmus_3341, retro_mmus_3446, retro_mmus_3545, retro_mmus_3581, retro_mmus_3712, retro_mmus_397, retro_mmus_400, retro_mmus_401, retro_mmus_598, retro_mmus_601, retro_mmus_606, retro_mmus_663, retro_mmus_734, retro_mmus_735, retro_mmus_758, retro_mmus_782, retro_mmus_806, retro_mmus_835, retro_mmus_862, retro_mmus_883, retro_mmus_918, retro_mmus_932, retro_mmus_940, retro_mmus_957, retro_mmus_993, retro_mmus_998,
Nomascus leucogenys ENSNLEG000000003276 retrocopies
Oryctolagus cuniculus ENSOCUG0000000250610 retrocopies
Otolemur garnettii ENSOGAG000000339364 retrocopies
Otolemur garnettii ENSOGAG000000344231 retrocopy
Pongo abelii ENSPPYG000000052337 retrocopies
Pongo abelii ENSPPYG000000061672 retrocopies
Pan troglodytes ENSPTRG000000057281 retrocopy
Pteropus vampyrus ENSPVAG0000000007782 retrocopies
Rattus norvegicus ENSRNOG0000000095713 retrocopies
Sorex araneus ENSSARG0000001312951 retrocopies
Sarcophilus harrisii ENSSHAG0000000084511 retrocopies
Sus scrofa ENSSSCG000000093039 retrocopies
Vicugna pacos ENSVPAG0000000620613 retrocopies



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