RetrogeneDB ID:

retro_mmul_1954

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:5:75169983..75170335(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.2942
Ensembl ID:ENSMMUG00000022881
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mmul_1954
CAGAAAGACAAGAAGCCCAAGAAGTCAACCTGGAAGTTTCATTTGGACCTTACTCATCCAGTAGAAGATGGAATTTTTGA
TTCTGGAAATTTTGAACAATTTCTATGGGAGAAGGTTAAAGTCAATGACAAAACTGGATATCTCGGGAATGTTGTTCACA
CTGAATGCTTCAAGAATAAAATCACATTCTTTCTCAGAAACAGTTCTCTAAAAGGTATTTGAAATACCTTACCAAGAAAT
ACCTTAAGAAGAGCAATCTTCATGATTGGCTTCGAGTGGTTGCATCTGACAGAAGACTTACGAACTTCATTACTTCCAGA
TTAGTCAAGAAGATGAATCAGAGTTGGAGGAC

ORF - retro_mmul_1954 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.3 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalQKDKKPKRSTWKFNLDLTHPVEDGIFDSGNFEQFLREKVKVNGKTGNLGNVVHIERFKNKIT-VVSEKQF
QKDKKPK.STWKF.LDLTHPVEDGIFDSGNFEQFL.EKVKVN.KTG.LGNVVH.E.FKNKIT...S.KQF
RetrocopyQKDKKPKKSTWKFHLDLTHPVEDGIFDSGNFEQFLWEKVKVNDKTGYLGNVVHTECFKNKIT<ILSQKQF
ParentalSKRYLKYLTKKYLKKNNLRDWLRVVASDK-ETYELRYFQISQDEDESESED
SKRYLKYLTKKYLKK.NL.DWLRVVASD...TYEL.YFQISQ.EDESE.ED
RetrocopySKRYLKYLTKKYLKKSNLHDWLRVVASDR<KTYELHYFQISQ-EDESELED

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






RNA-Seq - click to see more details

(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 .00 RPM 4 .26 RPM
SRP007412_brain_prefrontal_cortex 0 .00 RPM 2 .54 RPM
SRP007412_cerebellum 0 .00 RPM 2 .71 RPM
SRP007412_heart 0 .00 RPM 7 .54 RPM
SRP007412_kidney 0 .00 RPM 3 .64 RPM
SRP007412_liver 0 .00 RPM 4 .35 RPM
SRP007412_testis 0 .00 RPM 15 .00 RPM

ChIP-Seq - click to see more details

Macaca mulatta was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mmul_1954 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_1954 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_1954 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2929
Gorilla gorilla retro_ggor_2031
Pongo abelii retro_pabe_2524
Parental genes homology:
Parental genes homology involve 28 parental genes, and 93 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000047301 retrocopy
retro_amel_7,
Canis familiaris ENSCAFG000000149552 retrocopies
retro_cfam_1410, retro_cfam_773,
Callithrix jacchus ENSCJAG000000024271 retrocopy
retro_cjac_3983,
Cavia porcellus ENSCPOG000000092151 retrocopy
retro_cpor_1544,
Equus caballus ENSECAG000000188941 retrocopy
retro_ecab_728,
Erinaceus europaeus ENSEEUG000000119415 retrocopies
retro_eeur_436, retro_eeur_60, retro_eeur_602, retro_eeur_676, retro_eeur_691,
Echinops telfairi ENSETEG000000106589 retrocopies
retro_etel_1289, retro_etel_1433, retro_etel_1459, retro_etel_151, retro_etel_1680, retro_etel_335, retro_etel_513, retro_etel_800, retro_etel_936,
Homo sapiens ENSG000001635841 retrocopy
retro_hsap_2929,
Gorilla gorilla ENSGGOG000000017341 retrocopy
retro_ggor_2031,
Gadus morhua ENSGMOG000000040771 retrocopy
retro_gmor_10,
Loxodonta africana ENSLAFG000000132202 retrocopies
retro_lafr_1121, retro_lafr_682,
Macropus eugenii ENSMEUG000000094841 retrocopy
retro_meug_390,
Myotis lucifugus ENSMLUG000000230522 retrocopies
retro_mluc_1183, retro_mluc_1588,
Myotis lucifugus ENSMLUG000000276838 retrocopies
retro_mluc_1225, retro_mluc_1403, retro_mluc_1690, retro_mluc_1804, retro_mluc_1967, retro_mluc_2383, retro_mluc_2401, retro_mluc_668,
Macaca mulatta ENSMMUG0000001834712 retrocopies
retro_mmul_1004, retro_mmul_1044, retro_mmul_1047, retro_mmul_1512, retro_mmul_2209, retro_mmul_2264, retro_mmul_2467, retro_mmul_2601, retro_mmul_271, retro_mmul_445, retro_mmul_469, retro_mmul_80,
Macaca mulatta ENSMMUG00000022881 2 retrocopies
retro_mmul_1927, retro_mmul_1954 ,
Mus musculus ENSMUSG000000392214 retrocopies
retro_mmus_1380, retro_mmus_2633, retro_mmus_2674, retro_mmus_3631,
Nomascus leucogenys ENSNLEG000000052872 retrocopies
retro_nleu_1918, retro_nleu_2266,
Oryctolagus cuniculus ENSOCUG000000149622 retrocopies
retro_ocun_1, retro_ocun_256,
Otolemur garnettii ENSOGAG000000126422 retrocopies
retro_ogar_1434, retro_ogar_780,
Procavia capensis ENSPCAG000000087041 retrocopy
retro_pcap_105,
Pongo abelii ENSPPYG000000259001 retrocopy
retro_pabe_2524,
Pteropus vampyrus ENSPVAG000000115241 retrocopy
retro_pvam_328,
Rattus norvegicus ENSRNOG000000118172 retrocopies
retro_rnor_111, retro_rnor_2152,
Sus scrofa ENSSSCG000000274415 retrocopies
retro_sscr_1039, retro_sscr_129, retro_sscr_141, retro_sscr_85, retro_sscr_860,
Ictidomys tridecemlineatus ENSSTOG000000229723 retrocopies
retro_itri_1511, retro_itri_1533, retro_itri_492,
Tupaia belangeri ENSTBEG0000000035717 retrocopies
retro_tbel_1135, retro_tbel_1188, retro_tbel_2011, retro_tbel_2073, retro_tbel_2081, retro_tbel_226, retro_tbel_2325, retro_tbel_2333, retro_tbel_2434, retro_tbel_2936, retro_tbel_3526, retro_tbel_3796, retro_tbel_4070, retro_tbel_4372, retro_tbel_4573, retro_tbel_4681, retro_tbel_575,
Tursiops truncatus ENSTTRG000000070353 retrocopies
retro_ttru_1180, retro_ttru_168, retro_ttru_968,


Copyright © RetrogeneDB 2014-2017