RetrogeneDB ID:

retro_shar_664

Retrocopy
location
Organism:Tasmanian devil (Sarcophilus harrisii)
Coordinates:GL856966.1:485905..486339(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL21
Ensembl ID:ENSSHAG00000000845
Aliases:None
Description:ribosomal protein L21 [Source:HGNC Symbol;Acc:10313]


Retrocopy-Parental alignment summary:






>retro_shar_664
ATGATTAATACAAAAGAAAAAAGAAAAGGGACTTGAAATCTGTTCTCTAGGTCCTTGTGAAAATATAGTGTTGTCTTTTT
GGCTACGTAGATTCAAGTCTACAAGAAGAGGTATGTTGTAGATATCAAAAGCCTAAGGATAACTCAACAGGGAATATCCC
CAAAATGTTACCATGGCAAGACAGGTTGGGTCTAAGCTATTATTCAGCATATTGTAGGCACTGTTATAAACAAATTCAAG
GTCAAGATTCAAGTCAAATGAGTTAATGTGCACACTAAGCATATTAAGCCTTCTAAAGAGGAGAGCTTCCTGAATTATGT
AAAGGAAATGATCGGAAGGAAAAGGAAGCTGAAGATAAAGGCATCTGGGGTCAGTTGAGGTTTCAGCCTGCCTCCTCCAG
AGTAGCACACTTTGTGATGACAAATGGCAAGGAA

ORF - retro_shar_664 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 55.7 %
Parental protein coverage: 91.93 %
Number of stop codons detected: 5
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMTNTKGKRRGTRYMFSRPFRKHAGVVPLATYMRIYKKGDIVDIKGMGTVQQGMPHKCYHGKTGRVYNVTQ
M.NTK.KR.GT...FSR...K...VV.LAT....YKK...VDIK.....QQG...KCYHGKTG.V....Q
RetrocopyMINTKEKRKGT*NLFSRSL*KYS-VVFLAT*IQVYKKRYVVDIKSLRITQQGISPKCYHGKTGWV*AIIQ
ParentalHAVGIVVNKQVKGKILAKRINVRIEHIKHSKSRDSFLKRVKE-NDQKKKEAKEKGTWVQLKRQPAPPREA
H.VG.V.NK..K.KI..K..NV...HIK.SK...SFL..VKE.ND.K.KEA..KG.W.QL..QPA..R.A
RetrocopyHIVGTVINK-FKVKIQVK*VNVHTKHIKPSK-EESFLNYVKE<NDRKEKEAEDKGIWGQLRFQPASSRVA
ParentalHFVRTNGKQ
HFV.TNGK.
RetrocopyHFVMTNGKE

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Sarcophilus harrisii was not studied using RNA-Seq expression data.
Sarcophilus harrisii was not studied using ChIP-Seq data.
Sarcophilus harrisii was not studied using EST data.
Sarcophilus harrisii was not studied using FANTOM5 data.
retro_shar_664 was not experimentally validated.

Retrocopy orthology:
Sarcophilus harrisii 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 25 parental genes, and 527 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000031691 retrocopy
Bos taurus ENSBTAG000000016485 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
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
Pongo abelii ENSPPYG000000052337 retrocopies
Pan troglodytes ENSPTRG000000057281 retrocopy
Pteropus vampyrus ENSPVAG0000000007782 retrocopies
Rattus norvegicus ENSRNOG0000000095713 retrocopies
Sarcophilus harrisii ENSSHAG00000000845 11 retrocopies
Sus scrofa ENSSSCG000000093039 retrocopies
Vicugna pacos ENSVPAG0000000620613 retrocopies



Copyright © RetrogeneDB 2014-2017