RetrogeneDB ID:

retro_mmul_2518

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:X:92017077..92018359(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.10126
Ensembl ID:ENSMMUG00000009948
Aliases:None
Description:Histone deacetylase [Source:UniProtKB/TrEMBL;Acc:F6RIU8]


Retrocopy-Parental alignment summary:






>retro_mmul_2518
CGCCCTCACAAAGCCAATGCTGAGGAGATGACCAAGTACCATAGTGACGACTACATTAAATTCCTGCGCTCCATCCGTCC
AGATAACATGTCGGAGTACAGCAAGCAGATGCAGAGATTCAACCTTGGTGAGGACTGTCCAGTATTCAACGGCCTATTTG
AGTTCTGTCAGTTGTCTACCGGTGGTTCTGTGGCAAGTGCTGTGAAACTTAATAAGCAGCAGACGGACATGGCTGTGAAT
TGGGCTGGGGGCCTGCACCATGCAAAGAAGTCTGAGGCATCTGGCTTCTGTTACGTCAATAATACCGTCTTGGCCATTCT
GGAACTGCTAAAGCATCACCAGAGGGTGCTGTATATTGACATTGATGTTCACCATAGCGACGGCATGGAAGAGGCCTTCT
ATACCACAGACCGGGTCATGACTGTGTCCTTTCATAAGTATGGAGAGTACTTCCCAGGAACTGGGGACCTGTGGGATATC
GGGGCTGGCAAAGGCAAGTATTATGCTGTTAACTACCCGCTCCAAGACGGGATTGATGACAAGTCCTATGAGGCCATTTT
CAAGCCAGTCATGTCCAAAGTAATGGAGATGTTCCAGCCTAGCTCAGTGGTCTTACAGTGTGGCTCAGACTCCCTGTCTG
GGGATCGGTTAGGTTGCTTCAATCTAACCATCAAAGGGCACGCCAAGTGTGTGGAATTTGTCAAGAGCTTTAACCTGCCT
ATGCTGATGCTGGGAGGTGGTGATTACACCATTTGTAATGTTGCCCGGTGCTGGACATACGAGACAGCTGTGGCCCTGGA
TACGGAGATCCCTAATGAGCTTCCGTACAATGACTACTTTGAATACTTTGGACCAGATTTCAAGCTCCACATCAGTCCTT
CCAATATGACTAACCAGAACACGAATGAGTACCTGGAGAAGATCGAACAGCGACTGTTTGAGAACCTTAGAATGCTGCTG
CATGCACCTAGGGTCCAAATGCAGGCAATTCCTGAAGACGCCATCCCTGAGGAGAGTGGCGATGAGGACGAAGAAGACCC
TGATAAGCGCATCTCGATCTGCTCCTCCGACAAACGAATTGCCTGTGAGGAAGTTCTCCAATTCTGAAGAGGAAGGAGAG
GGGGGCCGCAAGAACTCTTCCAACTTCAAAAAAGCCAAGAGAGTCAAAACAGAGGATGAAAAAGAGAAAGACCCAGAGGA
GAAGAAAGAAGCCACAGAAGAGGAGAAAACCAAGGAGGAAAAGCCAGAAGCCAAAGGGGTCAAGGAGGAGGTCAAGTTGG
CC

ORF - retro_mmul_2518 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.74 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalRPHKANAEEMTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVASAVKL
RPHKANAEEMTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFN.GEDCPVF.GLFEFCQLSTGGSVASAVKL
RetrocopyRPHKANAEEMTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFNLGEDCPVFNGLFEFCQLSTGGSVASAVKL
ParentalNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVM
NKQQTD.AVNWAGGLHHAKKSEASGFCYVN..VLAILELLK.HQRVLYIDID.HH.DG.EEAFYTTDRVM
RetrocopyNKQQTDMAVNWAGGLHHAKKSEASGFCYVNNTVLAILELLKHHQRVLYIDIDVHHSDGMEEAFYTTDRVM
ParentalTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGSD
TVSFHKYGEYFPGTGDL.DIGAGKGKYYAVNYPL.DGIDD.SYEAIFKPVMSKVMEMFQPS.VVLQCGSD
RetrocopyTVSFHKYGEYFPGTGDLWDIGAGKGKYYAVNYPLQDGIDDKSYEAIFKPVMSKVMEMFQPSSVVLQCGSD
ParentalSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGGGYTIRNVARCWTYETAVALDTEIPNELPYNDYF
SLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGG.YTI.NVARCWTYETAVALDTEIPNELPYNDYF
RetrocopySLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGGDYTICNVARCWTYETAVALDTEIPNELPYNDYF
ParentalEYFGPDFKLHISPSNMTNQNTNEYLEKIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDEDEEDPDKR
EYFGPDFKLHISPSNMTNQNTNEYLEKI.QRLFENLRML.HAP.VQMQAIPEDAIPEESGDEDEEDPDKR
RetrocopyEYFGPDFKLHISPSNMTNQNTNEYLEKIEQRLFENLRMLLHAPRVQMQAIPEDAIPEESGDEDEEDPDKR
ParentalISICSSDKRIACEEEF-SDSEEEGEGGRKNSSNFKKAKRVKTEDEKEKDPEEKKEVTEEEKTKEEKPEAK
ISICSSDKRIACEE......EE.GEGGRKNSSNFKKAKRVKTE...................KEEKPEAK
RetrocopyISICSSDKRIACEEVL>NSEEE-GEGGRKNSSNFKKAKRVKTEXXXXXXXXXXXXXXXXXXXKEEKPEAK
ParentalGVKEEVKLA
GVKEEVKLA
RetrocopyGVKEEVKLA

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 .45 RPM 7 .62 RPM
SRP007412_brain_prefrontal_cortex 0 .48 RPM 7 .54 RPM
SRP007412_cerebellum 0 .19 RPM 5 .10 RPM
SRP007412_heart 0 .41 RPM 12 .37 RPM
SRP007412_kidney 1 .88 RPM 34 .86 RPM
SRP007412_liver 0 .67 RPM 24 .34 RPM
SRP007412_testis 6 .22 RPM 83 .64 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_2518 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_2518 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_2518 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 15 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Ciona intestinalis ENSCING000000026491 retrocopy
retro_cint_18,
Callithrix jacchus ENSCJAG000000009702 retrocopies
retro_cjac_2490, retro_cjac_830,
Homo sapiens ENSG000001164781 retrocopy
retro_hsap_826,
Gorilla gorilla ENSGGOG000000117411 retrocopy
retro_ggor_676,
Myotis lucifugus ENSMLUG000000138371 retrocopy
retro_mluc_283,
Macaca mulatta ENSMMUG00000009948 2 retrocopies
retro_mmul_1085, retro_mmul_2518 ,
Macaca mulatta ENSMMUG000000125881 retrocopy
retro_mmul_49,
Mus musculus ENSMUSG000000288001 retrocopy
retro_mmus_153,
Nomascus leucogenys ENSNLEG000000024731 retrocopy
retro_nleu_259,
Otolemur garnettii ENSOGAG000000057093 retrocopies
retro_ogar_2181, retro_ogar_3022, retro_ogar_3313,
Pelodiscus sinensis ENSPSIG000000041341 retrocopy
retro_psin_44,
Pteropus vampyrus ENSPVAG000000133251 retrocopy
retro_pvam_1339,
Rattus norvegicus ENSRNOG000000095683 retrocopies
retro_rnor_1091, retro_rnor_1098, retro_rnor_2457,
Sarcophilus harrisii ENSSHAG000000087871 retrocopy
retro_shar_573,
Tursiops truncatus ENSTTRG000000016131 retrocopy
retro_ttru_1236,


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