RetrogeneDB ID:

retro_ogar_1952

Retrocopy
location
Organism:Bushbaby (Otolemur garnettii)
Coordinates:GL873576.1:8441695..8443066(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOGAG00000025250
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSOGAG00000011740
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ogar_1952
ATGTCCATCAGAGTTATCCAGAAGTCCTACAAGGTGTCCACCTCCACCCCACAGGCCTTCAGCAGCCGCTCATACAGCAG
TGGGCCCGGTGCCCACATCCACTCCTCGAGCTTCTCTCGGGTGGGCAGTGGCAGCTTCTGGAGTGGCCTGGGCACCAGCC
TGGGTCTGGTTGGAGGCTACGTCAGAGCTGGAGATATGGGGGGCATCACAGCCGTCACAGTGAACCAGAGTCTGCTAAGC
CCACTCAACCTGGGGGTGGACCCCAACATTCAGGTCGTGCACACCCAGGAGAAGGAGATCAAGACCCTCAACAACAAGTT
TGCCTCCTTCATCGACAGGGTGCGCTTCCTGGAGCAGCAGAACAAGATGCTGGAGACCAAGTGGAACCTCCTGCAGCAGC
AGAAGACGGCTCGCAGCAACATGGACAGCATGTTTGAAAGCTACATCAACAACCTTCAGCGACAGCTGGACACACTGGGC
CAGGAGAAGCTGAAGCTGGAGGCAGAGCTTGGCAACATGCAGGGGCTGGTGGAGGACTTCAAGAATAAGTATGAGGTGGA
GACCAGCAAGCTACAGAGATGGAGAATGAATCTGTCCTCATCAAGAAGGATGTGGATGAAGCTACATGAACCAGGTGGAG
CTGGAGTCCGGCCTGGACGGGCTGACTGACGAAATCAACTTCCTCAGCAGCTGTATGAAGAGGAGATCCGTGAGCTGCAG
TCTCAGATCTCAGACACGTCTGTGGTCCTGTGCATGGACAATAGCTGCTCCCTGGACATGGACAGCATCCTTGCTGAGGT
CCGCACCCAGTACGAGGAGATCGCCAACCACAGCTGGGCTAAGGCTGAGAGCATGTACCAGACCAAGTACAAAGAGCTGC
AGGTGCAGGCTGGGAAGCACGGAACCAACTGCAGTGCAGGAAGACTGAGATCTCTGTCATGAACCAGAACATCAGCCAGC
TCCAGAAAGAGATGGAAGCTCTCAAAGGCCAGAGGGCTGCCCTGGAGGCCTCCATTGCGGATGCCAAGCAGTGTAGGGAG
CTGGCCCTTAAGGATGCCAACACCAAGCTGGCCCAGCTGGAGGCTGCCCTGCATCAAGCCAAGCAGGACATGGCTCAGCA
GCTGCGTGAATACCAGGATCTGATGAATGTCAAGCTGGCCCTGGACGTGGAGATCGCCACCTACTGCAAGCTGCTGGAGG
ATGAGGAGAGCCGGCCGGAGTCGGGATGCAGAGCATGAGTATCCACACGAAGACCACCAGTGGCTATTCGAGTGGCCTGA
GCTCGGCCTACAGAGACCTCACAAGCCTGGCCTCAGCTATGGTCTGAGCTCCTTCCAGACTGGCTTTGGCTCTGGTGGGG
GCACCAGCTCC

ORF - retro_ogar_1952 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.05 %
Parental protein coverage: 93.69 %
Number of stop codons detected: 0
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalMSIRVTQKSYKVSTSAPRAFSSRSYSSGPGARISSSSFSRVGSGSFRSGLSTGLGLGGGYAGAGGMGGIT
MSIRV.QKSYKVSTS.P.AFSSRSYSSGPGA.I.SSSFSRVGSGSF.SGL.T.LGL.GGY..AG.MGGIT
RetrocopyMSIRVIQKSYKVSTSTPQAFSSRSYSSGPGAHIHSSSFSRVGSGSFWSGLGTSLGLVGGYVRAGDMGGIT
ParentalAVTVNQSLLSPLNLEVDPNIQAVRTQEKEEIKTLNNKFASFIDKVRFLEQQNKMLETKWNLLQQQKTARS
AVTVNQSLLSPLNL.VDPNIQ.V.TQEKE.IKTLNNKFASFID.VRFLEQQNKMLETKWNLLQQQKTARS
RetrocopyAVTVNQSLLSPLNLGVDPNIQVVHTQEKE-IKTLNNKFASFIDRVRFLEQQNKMLETKWNLLQQQKTARS
ParentalNMDSMFESYINNLRRQLDTLGQEKLKLEAELGNMQGLVEDFKNKYEEEINK-RTEMENEFVLIKKDVDEA
NMDSMFESYINNL.RQLDTLGQEKLKLEAELGNMQGLVEDFKNKYE.E..K..TEMENE.VLIKKDVDEA
RetrocopyNMDSMFESYINNLQRQLDTLGQEKLKLEAELGNMQGLVEDFKNKYEVETSK<ATEMENESVLIKKDVDEA
Parental-YMNKVELESRLDGLTDEINFL-RQLYEEEIRELQSQISDTSVVLSMDNSRSLDMDSIIAEVRAQYEEIA
.YMN.VELES.LDGLTDEINFL..QLYEEEIRELQSQISDTSVVL.MDNS.SLDMDSI.AEVR.QYEEIA
Retrocopy<YMNQVELESGLDGLTDEINFL<QQLYEEEIRELQSQISDTSVVLCMDNSCSLDMDSILAEVRTQYEEIA
ParentalNRSRAEAESVYLTKYEELQVQAGKHG-DDLRRTKTEISDMNRNISRLQNEIEALKGQRAALEASIADAEQ
N.S.A.AES.Y.TKY.ELQVQAGKHG...L...KTEIS.MN.NIS.LQ.E.EALKGQRAALEASIADA.Q
RetrocopyNHSWAKAESMYQTKYKELQVQAGKHG<NQLQCRKTEISVMNQNISQLQKEMEALKGQRAALEASIADAKQ
ParentalRGELALKDANAKLAQLEAALRQAKQDMAQQLREYQDLMNVKLALDVEIATYRKLLEGEESRLES-GMQNM
..ELALKDAN.KLAQLEAAL.QAKQDMAQQLREYQDLMNVKLALDVEIATY.KLLE.EESR.ES.GMQ.M
RetrocopyCRELALKDANTKLAQLEAALHQAKQDMAQQLREYQDLMNVKLALDVEIATYCKLLEDEESRPES<GMQSM
ParentalSIHTKTTSGYSGGLSSAYGGLTS-PGLSYGLSSFQTGFGSGGGSSS
SIHTKTTSGYS.GLSSAY..LTS.PGLSYGLSSFQTGFGSGGG.SS
RetrocopySIHTKTTSGYSSGLSSAYRDLTS<PGLSYGLSSFQTGFGSGGGTSS

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






RNA-Seq - click to see more details

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Otolemur garnettii was not studied using ChIP-Seq data.

EST - click to see more details

Otolemur garnettii was not studied using EST data.

TSS - click to see more details

Otolemur garnettii was not studied using FANTOM5 data.

Lab - click to see more details

retro_ogar_1952 was not experimentally validated.

Retrocopy orthology:
Otolemur garnettii 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 16 parental genes, and 151 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000071992 retrocopies
retro_cfam_1036, retro_cfam_1590,
Callithrix jacchus ENSCJAG000000181473 retrocopies
retro_cjac_124, retro_cjac_167, retro_cjac_216,
Cavia porcellus ENSCPOG000000026155 retrocopies
retro_cpor_1269, retro_cpor_1459, retro_cpor_233, retro_cpor_302, retro_cpor_516,
Dasypus novemcinctus ENSDNOG000000074003 retrocopies
retro_dnov_1267, retro_dnov_1886, retro_dnov_2358,
Felis catus ENSFCAG000000002982 retrocopies
retro_fcat_1142, retro_fcat_891,
Homo sapiens ENSG0000017042128 retrocopies
retro_hsap_1012, retro_hsap_1024, retro_hsap_1324, retro_hsap_1513, retro_hsap_1557, retro_hsap_1599, retro_hsap_169, retro_hsap_1708, retro_hsap_235, retro_hsap_2354, retro_hsap_2669, retro_hsap_2731, retro_hsap_2768, retro_hsap_2797, retro_hsap_2842, retro_hsap_3069, retro_hsap_3359, retro_hsap_3379, retro_hsap_3433, retro_hsap_371, retro_hsap_3963, retro_hsap_4203, retro_hsap_4688, retro_hsap_4691, retro_hsap_4775, retro_hsap_644, retro_hsap_844, retro_hsap_932,
Gorilla gorilla ENSGGOG0000001467318 retrocopies
retro_ggor_1160, retro_ggor_1787, retro_ggor_1862, retro_ggor_1897, retro_ggor_1900, retro_ggor_2320, retro_ggor_2662, retro_ggor_2913, retro_ggor_2918, retro_ggor_297, retro_ggor_2975, retro_ggor_382, retro_ggor_564, retro_ggor_66, retro_ggor_691, retro_ggor_751, retro_ggor_803, retro_ggor_809,
Macaca mulatta ENSMMUG0000000216322 retrocopies
retro_mmul_1069, retro_mmul_1122, retro_mmul_1178, retro_mmul_1349, retro_mmul_1351, retro_mmul_1412, retro_mmul_1697, retro_mmul_1753, retro_mmul_1810, retro_mmul_1855, retro_mmul_1866, retro_mmul_2097, retro_mmul_2137, retro_mmul_2357, retro_mmul_2431, retro_mmul_2546, retro_mmul_289, retro_mmul_488, retro_mmul_58, retro_mmul_766, retro_mmul_816, retro_mmul_886,
Mustela putorius furoENSMPUG000000064417 retrocopies
retro_mputfur_1101, retro_mputfur_1208, retro_mputfur_1271, retro_mputfur_1557, retro_mputfur_1587, retro_mputfur_556, retro_mputfur_895,
Mus musculus ENSMUSG000000493821 retrocopy
retro_mmus_2905,
Nomascus leucogenys ENSNLEG000000177338 retrocopies
retro_nleu_1913, retro_nleu_225, retro_nleu_2285, retro_nleu_2421, retro_nleu_2485, retro_nleu_2727, retro_nleu_2787, retro_nleu_672,
Oryctolagus cuniculus ENSOCUG000000069451 retrocopy
retro_ocun_313,
Otolemur garnettii ENSOGAG00000011740 16 retrocopies
retro_ogar_1076, retro_ogar_1162, retro_ogar_1256, retro_ogar_1572, retro_ogar_1874, retro_ogar_1898, retro_ogar_1952 , retro_ogar_2004, retro_ogar_2149, retro_ogar_2177, retro_ogar_2261, retro_ogar_2500, retro_ogar_3198, retro_ogar_3318, retro_ogar_339, retro_ogar_664,
Pongo abelii ENSPPYG0000000456231 retrocopies
retro_pabe_1102, retro_pabe_1261, retro_pabe_1289, retro_pabe_1460, retro_pabe_1743, retro_pabe_2063, retro_pabe_2077, retro_pabe_2129, retro_pabe_2142, retro_pabe_2214, retro_pabe_2270, retro_pabe_2352, retro_pabe_2544, retro_pabe_2741, retro_pabe_2763, retro_pabe_2787, retro_pabe_2842, retro_pabe_2926, retro_pabe_2943, retro_pabe_3138, retro_pabe_332, retro_pabe_3439, retro_pabe_3644, retro_pabe_3716, retro_pabe_417, retro_pabe_460, retro_pabe_569, retro_pabe_605, retro_pabe_701, retro_pabe_803, retro_pabe_851,
Pteropus vampyrus ENSPVAG000000093603 retrocopies
retro_pvam_1299, retro_pvam_1396, retro_pvam_45,
Rattus norvegicus ENSRNOG000000097791 retrocopy
retro_rnor_807,


Copyright © RetrogeneDB 2014-2017