RetrogeneDB ID:

retro_btau_976

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:22:43937593..43938073(+)
Located in intron of:ENSBTAG00000021164
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL21
Ensembl ID:ENSBTAG00000001648
Aliases:RPL21, RPL21P16
Description:60S ribosomal protein L21 [Source:RefSeq peptide;Acc:NP_001178341]


Retrocopy-Parental alignment summary:






>retro_btau_976
ATGACCAACACAAAGGGAAAGAGGCGGGGCACCCGCTACATGTTCTCCAGGCCTTTCAGAAAACATGGAGTTGTTCCTTT
GGCCACATACATGCGAATCTACAGGAAGTGTGATATTGTAGATATCAAGGGAATGGGTACTGTTCAAAAAGGAATGCCCC
ACAAATGTTACCATGGCAAAACTGGAAGAGTCTACAATGTCACCCAGCATGCTGTTGGCATCATTGTAAACAAACAAGTT
AAGGGCAAGATTCTTGCCAAGAGAATTAATGTGCATATCGAGCATATTAAGCACTCTAAGAGCTGAGATAGCTTCTTGAA
ATGTGTGAAGGAAAATGATCAGAAAAAGAAGGAAGCCAAAGAGAAAGGGACTTGGGTTCAGCTGAAGCGCCAGCCTGCTC
CACCCAGAGAAGCACACTTTGAGAGGACCAATGGAAAGGAACCCGAACTGTTGGAGCCCATTCCCTATGAATTCATGGCC

ORF - retro_btau_976 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.88 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMTNTKGKRRGTRYMFSRPFRKHGVVPLATYMRIYRKGDIVDIKGMGTVQKGMPHKCYHGKTGRVYNVTQH
MTNTKGKRRGTRYMFSRPFRKHGVVPLATYMRIYRK.DIVDIKGMGTVQKGMPHKCYHGKTGRVYNVTQH
RetrocopyMTNTKGKRRGTRYMFSRPFRKHGVVPLATYMRIYRKCDIVDIKGMGTVQKGMPHKCYHGKTGRVYNVTQH
ParentalAVGIIVNKQVKGKILAKRINVRIEHIKHSKSRDSFLKRVKENDQKKKEAKEKGTWVQLKRQPAPPREAHF
AVGIIVNKQVKGKILAKRINV.IEHIKHSKS.DSFLK.VKENDQKKKEAKEKGTWVQLKRQPAPPREAHF
RetrocopyAVGIIVNKQVKGKILAKRINVHIEHIKHSKS*DSFLKCVKENDQKKKEAKEKGTWVQLKRQPAPPREAHF
ParentalVRTNGKEPELLEPIPYEFMA
.RTNGKEPELLEPIPYEFMA
RetrocopyERTNGKEPELLEPIPYEFMA

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
ERP005899_liver 70 .29 RPM 449 .16 RPM
ERP005899_muscle 224 .93 RPM 1634 .83 RPM
SRP017611_brain 22 .84 RPM 138 .23 RPM
SRP017611_kidney 61 .41 RPM 275 .14 RPM
SRP017611_liver 37 .23 RPM 215 .88 RPM
SRP030211_testis 20 .49 RPM 182 .25 RPM
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_976 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_976 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_976 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 ENSBTAG00000001648 5 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 ENSMUSG00000041453101 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



Copyright © RetrogeneDB 2014-2017