RetrogeneDB ID:

retro_mmul_1246

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:16:10466490..10466932(-)
Located in intron of:ENSMMUG00000004872
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.2413
Ensembl ID:ENSMMUG00000005082
Aliases:None
Description:mago-nashi homolog B [Source:RefSeq peptide;Acc:NP_001252545]


Retrocopy-Parental alignment summary:






>retro_mmul_1246
GCCATCCAGAGTGACTTTTATCTACATTACTACGTGGGGCACAAGGGCAAGTTCAGCCACGAGTTTCTGGAGTTTGAGTT
CTGACCAGACGGGAAATTAAGATAAGCCAACAACAGCAATTGTAAGAATGATGTCATGATCAGAAAAGAGGCTTATGTAC
ATAAAAGTGTGATGGAGGAACTGAAGAGTATAATTTATGACAGGGAAATTATCAAAGAGGATGATGCATTATGGCCTCCT
CCCAACCAAGTGGGCTGGCAGGAGCTTGAAATCGTTATTGGAGATGAACACATTTCTTTTACAACATCAAAAATTGGTTC
CCTTATTGATGTAAATCAATCCAAGGATCTGGAGGGCTTACGAGTATTTTATTATCTATGCCCAGGACCTGAAGTGTTTG
GTCTTCAGTCTTACTGGATTACACTTCAAGATTAAACCAATC

ORF - retro_mmul_1246 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.84 %
Parental protein coverage: 99.32 %
Number of stop codons detected: 2
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalAMASDFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIIDDSEI
A..SDFYL.YYVGHKGKF.HEFLEFEF.PDGKLR.ANNSN.KNDVMIRKEAYVHKSVMEELK.II.D.EI
RetrocopyAIQSDFYLHYYVGHKGKFSHEFLEFEF*PDGKLR*ANNSNCKNDVMIRKEAYVHKSVMEELKSIIYDREI
ParentalTKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLRVFYYL-VQDLKCLVFSLIG
.KEDDALWPPP..VG.QELEIVIGDEHISFTTSKIGSLIDVNQSKD.EGLRVFYYL..QDLKCLVFSL.G
RetrocopyIKEDDALWPPPNQVGWQELEIVIGDEHISFTTSKIGSLIDVNQSKDLEGLRVFYYL>AQDLKCLVFSLTG
ParentalLHFKIKPI
LHFKIKPI
RetrocopyLHFKIKPI

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 .78 RPM 2 .47 RPM
SRP007412_brain_prefrontal_cortex 0 .16 RPM 1 .90 RPM
SRP007412_cerebellum 1 .29 RPM 3 .42 RPM
SRP007412_heart 0 .12 RPM 3 .95 RPM
SRP007412_kidney 0 .35 RPM 2 .46 RPM
SRP007412_liver 0 .28 RPM 1 .35 RPM
SRP007412_testis 0 .49 RPM 3 .84 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_1246 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_1246 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_1246 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1803
Pan troglodytes retro_ptro_1179
Gorilla gorilla retro_ggor_1326
Pongo abelii retro_pabe_1479
Parental genes homology:
Parental genes homology involve 18 parental genes, and 45 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000192351 retrocopy
retro_btau_399,
Choloepus hoffmanni ENSCHOG000000043821 retrocopy
retro_chof_1730,
Callithrix jacchus ENSCJAG000000216627 retrocopies
retro_cjac_1336, retro_cjac_1840, retro_cjac_1858, retro_cjac_2354, retro_cjac_3234, retro_cjac_3250, retro_cjac_546,
Dasypus novemcinctus ENSDNOG000000059974 retrocopies
retro_dnov_140, retro_dnov_347, retro_dnov_423, retro_dnov_891,
Echinops telfairi ENSETEG000000165913 retrocopies
retro_etel_1022, retro_etel_1566, retro_etel_2147,
Homo sapiens ENSG000001111961 retrocopy
retro_hsap_1360,
Macropus eugenii ENSMEUG000000017821 retrocopy
retro_meug_324,
Myotis lucifugus ENSMLUG000000035272 retrocopies
retro_mluc_1039, retro_mluc_2484,
Macaca mulatta ENSMMUG00000005082 1 retrocopy
retro_mmul_1246 ,
Monodelphis domestica ENSMODG000000004621 retrocopy
retro_mdom_424,
Nomascus leucogenys ENSNLEG000000033551 retrocopy
retro_nleu_1395,
Ochotona princeps ENSOPRG000000005482 retrocopies
retro_opri_1171, retro_opri_308,
Pan troglodytes ENSPTRG000000046792 retrocopies
retro_ptro_1179, retro_ptro_932,
Sus scrofa ENSSSCG000000006351 retrocopy
retro_sscr_971,
Ictidomys tridecemlineatus ENSSTOG000000008351 retrocopy
retro_itri_212,
Tupaia belangeri ENSTBEG000000148207 retrocopies
retro_tbel_1250, retro_tbel_1393, retro_tbel_210, retro_tbel_2259, retro_tbel_2723, retro_tbel_2878, retro_tbel_451,
Tarsius syrichta ENSTSYG000000104527 retrocopies
retro_tsyr_1730, retro_tsyr_1748, retro_tsyr_383, retro_tsyr_658, retro_tsyr_81, retro_tsyr_908, retro_tsyr_966,
Tursiops truncatus ENSTTRG000000012722 retrocopies
retro_ttru_515, retro_ttru_647,


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