RetrogeneDB ID:

retro_mmul_1307

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:17:17759721..17760297(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.235
Ensembl ID:ENSMMUG00000008294
Aliases:None
Description:thioredoxin-dependent peroxide reductase, mitochondrial [Source:RefSeq peptide;Acc:NP_001252755]


Retrocopy-Parental alignment summary:






>retro_mmul_1307
TCCTCAGAAACCTACTATTGTAAGTATATTGCCATTGCCAGGGAAGAGTTCAAAGAACTAAGCCTTGACTTTAGGCTTGA
CTTAAAAAAGTATTTCATGCTCTTCTCTTATCCTTTGCCATTCACCTTTGTGTGTCCTACAGAAATTATTGCTTTGAGTG
AGACAGCCAACGCATTTCATACTGTGAACTGTGAAGTTGTTGCAGTTTCAGTGGATTTTCATTATAACCATCACGTCTAG
ATACATACACCAAAGAAAGCCAGTTTGGGCCATACGAGCATTGTACTCTTGTCAGACTTAAATAAATAGATTTCCTGAGA
CTATGATGTGCCGGTAGGAGGTCCTGACCTTCCACTAACGGGTCTTTTCATAATAGAACCCCAGTGGAAATCATCAAGTA
TATGAGTGTCAATGATCTCCCAATGGCTGAAGCATGGAAGAGACTGCCTTCTTCGTGAAGGCATGCCAGTTGGTGGAGAT
CCACAGAGAAGTCTGCCTGGCAAATAGATATTGAGTTCTCCTACAACCAAGCCAAATCCCACTGCTTCCAAAAAATACTT
TGAGAAGAAAAGTCAG

ORF - retro_mmul_1307 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 55.61 %
Parental protein coverage: 80.25 %
Number of stop codons detected: 6
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalSKHAPYFKGTAVVNGEFKDLSLD---DFKGKYLVLFFYPLDFTFVCPTEIVAFSDKANEFHDVNCEVVAV
S....Y.K..A....EFK.LSLD...D.K.KY..LF.YPL.FTFVCPTEI.A.S..AN.FH.VNCEVVAV
RetrocopySSETYYCKYIAIAREEFKELSLDFRLDLK-KYFMLFSYPLPFTFVCPTEIIALSETANAFHTVNCEVVAV
ParentalSVDSHFSHLAWINTPRKNGGLGHMNIALLSDLTKQISRDYGVLLEGPGLALRGLFIIDPNGVIKHLSVND
SVD.H..H...I.TP.K...LGH..I.LLSDL.K.IS.DY.V...GP.L.L.GLFII.P........V..
RetrocopySVDFHYNHHV*IHTPKK-ASLGHTSIVLLSDLNK*IS*DYDVPVGGPDLPLTGLFIIEPQWKSSSI*VSM
ParentalL-PVGRSVEETLRLVKAFQYVETHGEVC-PADWTPDSPTIKPNPAASKEYFQKVNQ
..P.G.S.EET...VKA.Q.VE.H.EVC.P......SPT.KPNP.ASK.YF.K..Q
RetrocopyI>PNG*SMEETAFFVKACQLVEIHREVC<PGK*ILSSPTTKPNPTASKKYFEKKSQ

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 65 .55 RPM
SRP007412_brain_prefrontal_cortex 0 .00 RPM 56 .96 RPM
SRP007412_cerebellum 0 .00 RPM 62 .06 RPM
SRP007412_heart 0 .00 RPM 78 .97 RPM
SRP007412_kidney 3 .99 RPM 187 .79 RPM
SRP007412_liver 0 .00 RPM 84 .91 RPM
SRP007412_testis 0 .15 RPM 12 .93 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_1307 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_1307 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_1307 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1253
Gorilla gorilla retro_ggor_986
Parental genes homology:
Parental genes homology involve 25 parental genes, and 48 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000087311 retrocopy
retro_btau_562,
Canis familiaris ENSCAFG000000121093 retrocopies
retro_cfam_1322, retro_cfam_219, retro_cfam_9,
Callithrix jacchus ENSCJAG000000196363 retrocopies
retro_cjac_1333, retro_cjac_3082, retro_cjac_653,
Ciona savignyi ENSCSAVG000000012091 retrocopy
retro_csav_6,
Dasypus novemcinctus ENSDNOG000000013593 retrocopies
retro_dnov_1052, retro_dnov_2373, retro_dnov_745,
Equus caballus ENSECAG000000170261 retrocopy
retro_ecab_408,
Erinaceus europaeus ENSEEUG000000092991 retrocopy
retro_eeur_238,
Homo sapiens ENSG000001656723 retrocopies
retro_hsap_1253, retro_hsap_2587, retro_hsap_2653,
Gorilla gorilla ENSGGOG000000263641 retrocopy
retro_ggor_986,
Macropus eugenii ENSMEUG000000077323 retrocopies
retro_meug_1219, retro_meug_1735, retro_meug_62,
Microcebus murinus ENSMICG000000076271 retrocopy
retro_mmur_475,
Myotis lucifugus ENSMLUG000000128713 retrocopies
retro_mluc_1203, retro_mluc_1522, retro_mluc_2069,
Macaca mulatta ENSMMUG000000056892 retrocopies
retro_mmul_1780, retro_mmul_2061,
Macaca mulatta ENSMMUG000000062211 retrocopy
retro_mmul_762,
Macaca mulatta ENSMMUG00000008294 2 retrocopies
retro_mmul_1307 , retro_mmul_1517,
Macaca mulatta ENSMMUG000000213661 retrocopy
retro_mmul_2001,
Monodelphis domestica ENSMODG000000092861 retrocopy
retro_mdom_1062,
Mustela putorius furoENSMPUG000000030741 retrocopy
retro_mputfur_1032,
Nomascus leucogenys ENSNLEG000000166983 retrocopies
retro_nleu_1521, retro_nleu_2118, retro_nleu_2453,
Oryctolagus cuniculus ENSOCUG000000173342 retrocopies
retro_ocun_135, retro_ocun_1434,
Pongo abelii ENSPPYG000000027001 retrocopy
retro_pabe_1906,
Pan troglodytes ENSPTRG000000029921 retrocopy
retro_ptro_29,
Ictidomys tridecemlineatus ENSSTOG000000025372 retrocopies
retro_itri_1098, retro_itri_1753,
Tupaia belangeri ENSTBEG000000110645 retrocopies
retro_tbel_3138, retro_tbel_3994, retro_tbel_710, retro_tbel_770, retro_tbel_811,
Tursiops truncatus ENSTTRG000000108782 retrocopies
retro_ttru_1703, retro_ttru_881,




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