RetrogeneDB ID:

retro_mmul_1380

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:19:52536494..52538034(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CLPX
Ensembl ID:ENSMMUG00000006714
Aliases:None
Description:ATP-dependent Clp protease ATP-binding subunit clpX-like, mitochondrial [Source:RefSeq peptide;Acc:NP_001247816]


Retrocopy-Parental alignment summary:






>retro_mmul_1380
GAGACCTTTGTGTCATCCACCCGTTTTGTCAAGTATGAAAAATGTCATCATTTTTTTGTTGTGCTATCTGAAGCAGACTC
AAAGAAAAGCATAATTAAAGAAACTGCATCAGCAGCAGAAGCTGTAAAATTGGCATTCCAACAGAAACCACCACCTCCCC
CTGAGAAGATTTATAACTACCTCGACAAGTATGTTGTTGGCCAGTCATTTGCTAAGAAGGTGCTTTCAGTTGCTGTGTAC
AATCATTATAAGAGAATACATAATAATATCCCAGCTAATCTGAGACAGCAAGCAGAGGTTGAGAAGCAGACATCATTAAC
ACCAAGAGAGTTAGAAGTAAGAAGACGGGAGGATGAGTACAGATTTACAAAATTACTTCAGATTGCTGGAATGAGCCCAC
ATGGTAATGCTTTAGGAGCATCAATGCAGCAACAGGTAAATCAACAGATACCTCAGGAAAAATGAGGAGGTGAAGTATTG
GATTCTTCTCATGATGACAGAAAACTTGAAAAAAGTAATATTTTGCTACTTGGACCAACTGGGTCAGGTAAAACTCTGCT
GGCACAAACCCTAGCTGAATGCCTTGATGTCCGTTTTGCTGTCTGTGACTGTACAACTATGACTCAGGCTGGATACGTAG
GCGAGGATATTGAATCTGTGATTGCCAAACTACTCCAAGATGCCAATTACAGTGTGGAAAAAGCACAACAAGGAATTGAT
GAAGTCGATAAGATTGGCAGTGTGCCAGGCGTTCATCAGTTACGAAATGTAGGTGAAGAAGGCGTTCAGCAAGGCTTATT
AAAACTACTAGAAGGCACAATAGTCAATGTTCCAGAAAAGAATTCCCGAAAGCTCCATGGAGAAACAGTACAAGTTGATA
CAACAAACATCCTGTTTGTTGCATCTGGTGCTTTCAGTGGTTTAGACAGAATCATCAGCAGGAGGAAAAATGAAAAGTAT
CTTGGATTTGGAACACCATCTAATCTGGGAAAGGGCAGAAGGGCTACAGCTGCTGCAGACCTTGCTAATAAAGTGGGGAA
TCAAATACGAAGACATTGAAGAAAAAGATCGGTTATTGCGTCATGTGGAAGCCAGAGGTCTGATTGAGTTTGGCATGATT
CCTGAGTTTGTGGGACAGTTGCCTGTGGTGGTTCCATTGCATAGCCTAGATGAGAAAACACTTGTACAAGTACTAACTGA
GCCACGAAATGCTGTTATTTCTCAGTACCAGGCCTTATTCAGCATGGATAAGTGTGAACTGAATGTTACTGAGGATGCTT
TGAAAGCTATAGCCAGATTGGCACTAGAATGAAAAACAGGTGCACAAGGCCTTCAGTCCATAATGGAAAAACTGTTACTA
GAACCAATGTTTGAAGTCCCTAATTCTGATATCGTACGTGTGGAGGTTGACAAAGAAGTAGTAGAAGGAAAAAAGGAACC
AGGATACATCCGGGCTCCAACGAAAGAATACTCTGAAGAGGAGTATGACTCTGGAGTTGAAGAAGAAGGCTGGCCCCGCC
AAGCAGATGCTGCAAATAGC

ORF - retro_mmul_1380 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.12 %
Parental protein coverage: 81.83 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalETFVSSTRFVKCEKCHHFFVVLSEADSKKSIIKEPESAAEAVKLAFQQKPPPPPKKIYNYLDKYVVGQSF
ETFVSSTRFVK.EKCHHFFVVLSEADSKKSIIKE..SAAEAVKLAFQQKPPPPP.KIYNYLDKYVVGQSF
RetrocopyETFVSSTRFVKYEKCHHFFVVLSEADSKKSIIKETASAAEAVKLAFQQKPPPPPEKIYNYLDKYVVGQSF
ParentalAKKVLSVAVYNHYKRIYNNIPANLRQQAEVEKQTSLTPRELEIRRREDEYRFTKLLQIAGISPHGNALGA
AKKVLSVAVYNHYKRI.NNIPANLRQQAEVEKQTSLTPRELE.RRREDEYRFTKLLQIAG.SPHGNALGA
RetrocopyAKKVLSVAVYNHYKRIHNNIPANLRQQAEVEKQTSLTPRELEVRRREDEYRFTKLLQIAGMSPHGNALGA
ParentalSMQQQVNQQIPQEKRGGEVLDSSHDDIKLEKSNILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQA
SMQQQVNQQIPQEK.GGEVLDSSHDD.KLEKSNILLLGPTGSGKTLLAQTLA.CLDV.FA.CDCTT.TQA
RetrocopySMQQQVNQQIPQEK*GGEVLDSSHDDRKLEKSNILLLGPTGSGKTLLAQTLAECLDVRFAVCDCTTMTQA
ParentalGYVGEDIESVIAKLLQDANYNVEKAQQGIVFLDEVDKIGSVPGIHQLRDVGGEGVQQGLLKLLEGTIVNV
GYVGEDIESVIAKLLQDANY.VEKAQQGI...DEVDKIGSVPG.HQLR.VG.EGVQQGLLKLLEGTIVNV
RetrocopyGYVGEDIESVIAKLLQDANYSVEKAQQGI---DEVDKIGSVPGVHQLRNVGEEGVQQGLLKLLEGTIVNV
ParentalPEKNSRKLRGETVQVDTTNILFVASGAFNGLDRIISRRKNEKYLGFGTPSNLGKGRRAAAAADLANR-SG
PEKNSRKL.GETVQVDTTNILFVASGAF.GLDRIISRRKNEKYLGFGTPSNLGKGRRA.AAADLAN..SG
RetrocopyPEKNSRKLHGETVQVDTTNILFVASGAFSGLDRIISRRKNEKYLGFGTPSNLGKGRRATAAADLANK<SG
ParentalESNTHQDIEEK-DRLLRHVEARDLIEFGMIPEFVGRLPVVVPLHSLDEKTLVQILTEPRNAVIPQYQALF
ESNT......K.DRLLRHVEAR.LIEFGMIPEFVG.LPVVVPLHSLDEKTLVQ.LTEPRNAVI.QYQALF
RetrocopyESNT-KTLKKK<DRLLRHVEARGLIEFGMIPEFVGQLPVVVPLHSLDEKTLVQVLTEPRNAVISQYQALF
ParentalSMDKCELNVTEDALKAIARLALERKTGARGLRSIMEKLLLEPMFEVPNSDIVCVEVDKEVVEGKKEPGYI
SMDKCELNVTEDALKAIARLALE.KTGA.GL.SIMEKLLLEPMFEVPNSDIV.VEVDKEVVEGKKEPGYI
RetrocopySMDKCELNVTEDALKAIARLALE*KTGAQGLQSIMEKLLLEPMFEVPNSDIVRVEVDKEVVEGKKEPGYI
ParentalRAPTKESSEEEYDSGVEEEGWPRQADAANS
RAPTKE.SEEEYDSGVEEEGWPRQADAANS
RetrocopyRAPTKEYSEEEYDSGVEEEGWPRQADAANS

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 27 .68 RPM
SRP007412_brain_prefrontal_cortex 0 .00 RPM 18 .40 RPM
SRP007412_cerebellum 0 .06 RPM 25 .89 RPM
SRP007412_heart 0 .12 RPM 24 .50 RPM
SRP007412_kidney 0 .00 RPM 33 .45 RPM
SRP007412_liver 0 .24 RPM 30 .99 RPM
SRP007412_testis 0 .53 RPM 142 .44 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_1380 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_1380 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_1380 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Macaca mulatta ENSMMUG00000006714 1 retrocopy
retro_mmul_1380 ,




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