RetrogeneDB ID:

retro_ptro_400

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:1:220988750..220990706(-)
Located in intron of:ENSPTRG00000002165
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CHM
Ensembl ID:ENSPTRG00000022071
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_400
ATGGCGGACAATCTTCCCACAGAGTTTGATGTGGTTATAATAGGGACAGGTTTGCCCGAATCCATCCTTGCAGCTGCATG
TTCAAGAAGTGGTCAGAGTGTTCTGCATATTGATTCAAGAAGCTACTATGGAGGAAACTGGGCTAGTTTCAGCTTTTCAG
GATTGCTATCCTGGTTGAAGGAGTATCAGCAAAACAATGACATTGGGGAAGAAAGTACTGTTGTATGGCAGGACCTGATC
CATGAAACAGAAGAAGCCATCACTCTTCGCAAGAAGGATGAAACTATTCAACACACAGAAGCTTTTTGCTACGCCAGTCA
GGATATGGAGGACAACGTTGAAGAGATTGGTGCTCTGCAGAAAAATCCTTCTTTGGGGGTGTCTAATACCTTCACTGAAG
TTCTGGATTCTGCATTGCCCGAAGAAAGCCAGTCATCATATTTTAATAGCGACGAAATGCCTGCAAAACACACTCAGAAA
AGTGATACAGAGATTTCACTAGAAGTAACTGATGTAGAGGAATCAGTGGAGAAGGAAAAGTATTGTGGAGATAAAACTTG
TATGCACACAGTTTCAGATAAAGATGGAGATAAAGATGAAAGCAAATCTACAGTAGAAGATAAGGCCGATGAACCAATTA
GAAATAGGATTACTTACTCTCAAATAGTTAAAGAAGGCAGGAGGTTTAATATTGATTTGGTGTCAAAACTGTTGTATTCT
CAAGGATTGCTAATTGATCTTTTAATCAAATCAGATGTTAGTCGTTATGTAGAATTTAAAAATGTCACTAGGATTCTTGC
ATTTCGGGAAGGAAAGGTAGAACAAGTTCCTTGTTCCAGAGCAGATGTCTTTAATAGCAAGGAACTCACCATGGTTGAAA
AGAGGATGCTAATGAAATTTCTCACATTTTGTTTAGAGTATGAACAACATCCTGATGAATACCAAGCTTTCAGGCAGTGT
TCATTTTCAGAATACTTAAAAACTAAAAAACTAACTCCCAACCTTCAACATTTTGTACTGCACTCAATTGCAATGACATC
AGAATCATCTTGCACTACAATAGATGGTCTTAACGCAACTAAAAACTTCCTTCAGTGTCTCGGACGGTTTGGCAACACTC
CCTTTTTATTTCCCTTGTATGGCCAAGGAGAAATTCCCCAGGGTTTCTGTAGGATGTGTGCAGTTTTTGGTGGAATCTAT
TGTCTTCGTCATAAAGTACAATGCTTTGTAGTCGACAAAGAATCTGGACGATGTAAAGCAATTATAGATCACTTTGGTCA
AAGAATAAATGCTAAATATTTTATTGTGGAAGACAGTTACCTTTCTGAGGAAACATGCTCAAATGTGCAGTATAAGCAGA
TCTCTAGGGCAGTACTCATTACAGATCAGTCTATACTAAAGACAGATTTAGATCAGCAGACTTCCATTCTGATAGTTCCT
CCAGCAGAGCCAGGAGCTTGTGCTGTACGGGTCACAGAATTATGTTCTTCAACCATGACATGCATGAAGGACACCTATCT
GGTACATTTGACATGTTCATCTTCTAAAACAGCAAGAGAAGACCTAGAATCAGTGGTGAAGAAATTATTCACTCCGTATA
CTGAAACAGAAATAAACGAGGAAGAACTTACAAAGCCAAGACTCTTGTGGGCTCTTTATTTTAATATGAGAGATTCCTCG
GGAATCAGCAGAAGCTTGTATAATGGCTTGCCTTCCAATGTTTATGTCTGCTCTGGGCCTGACTGTGGCCTGGGAAATGA
GCATGCTGTCAAGCAAGCTGAAACACTTTTCCAGGAGATCTTTCCAACTGAAGAATTCTGCCCTCCACCTCCAAATCCAG
AAGACGTTATCTTTGATGGTGATGATAAGCAGCCAGAGACTCCTGGAACCAATAATGTAGTAATGGCCAAACTAGAATCC
TCTGAGGAAAGCAAAAACCTGGAAAGCCCAGAGAAG

ORF - retro_ptro_400 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.82 %
Parental protein coverage: 99.54 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMADTLPSEFDVIVIGTGLPESIIAAACSRSGRRVLHVDSRSYYGGNWASFSFSGLLSWLKEYQENSDIVS
MAD.LP.EFDV..IGTGLPESI.AAACSRSG..VLH.DSRSYYGGNWASFSFSGLLSWLKEYQ.N.DI..
RetrocopyMADNLPTEFDVVIIGTGLPESILAAACSRSGQSVLHIDSRSYYGGNWASFSFSGLLSWLKEYQQNNDIGE
ParentalDSPV-WQDQILENEEAIALSRKDKTIQHVEVFCYASQDLHEDVEEAGALQKNHALVTSANSTEAADSAFL
.S.V.WQD.I.E.EEAI.L..KD.TIQH.E.FCYASQD....VEE.GALQKN..L..S...TE..DSA.L
RetrocopyESTVVWQDLIHETEEAITLRKKDETIQHTEAFCYASQDMEDNVEEIGALQKNPSLGVSNTFTEVLDSA-L
ParentalPTEDESLSTMSCEMLTEQTPSSDPENALEVNGAEVTGEKENHCDDKTCVPSTSAED--MSENVPIAEDTT
P.E..S....S.EM....T..SD.E..LEV...E...EKE..C.DKTC....S..D....E.....ED..
RetrocopyPEESQSSYFNSDEMPAKHTQKSDTEISLEVTDVEESVEKEKYCGDKTCMHTVSDKDGDKDESKSTVEDKA
ParentalEQPKKNRITYSQIIKEGRRFNIDLVSKLLYSRGLLIDLLIKSNVSRYAEFKNITRILAFREGRVEQVPCS
..P..NRITYSQI.KEGRRFNIDLVSKLLYS.GLLIDLLIKS.VSRY.EFKN.TRILAFREG.VEQVPCS
RetrocopyDEPIRNRITYSQIVKEGRRFNIDLVSKLLYSQGLLIDLLIKSDVSRYVEFKNVTRILAFREGKVEQVPCS
ParentalRADVFNSKQLTMVEKRMLMKFLTFCMEYEKYPDEYKGYEEITFYEYLKTQKLTPNLQYIVMHSIAMTSET
RADVFNSK.LTMVEKRMLMKFLTFC.EYE..PDEY.......F.EYLKT.KLTPNLQ..V.HSIAMTSE.
RetrocopyRADVFNSKELTMVEKRMLMKFLTFCLEYEQHPDEYQAFRQCSFSEYLKTKKLTPNLQHFVLHSIAMTSES
ParentalASSTIDGLKATKNFLHCLGRYGNTPFLFPLYGQGELPQCFCRMCAVFGGIYCLRHSVQCLVVDKESRKCK
...TIDGL.ATKNFL.CLGR.GNTPFLFPLYGQGE.PQ.FCRMCAVFGGIYCLRH.VQC.VVDKES..CK
RetrocopySCTTIDGLNATKNFLQCLGRFGNTPFLFPLYGQGEIPQGFCRMCAVFGGIYCLRHKVQCFVVDKESGRCK
ParentalAIIDQFGQRIISEHFLVEDSYFSENMCSRVQYRQISRAVLITDRSVLKTDSDQQISILTVPAEEPGTFAV
AIID.FGQRI....F.VEDSY.SE..CS.VQY.QISRAVLITD.S.LKTD.DQQ.SIL.VP..EPG..AV
RetrocopyAIIDHFGQRINAKYFIVEDSYLSEETCSNVQYKQISRAVLITDQSILKTDLDQQTSILIVPPAEPGACAV
ParentalRVIELCSSTMTCMKGTYLVHLTCTSSKTAREDLESVVQKLFIPYTEMEIENEQVEKPRILWALYFNMRDS
RV.ELCSSTMTCMK.TYLVHLTC.SSKTAREDLESVV.KLF.PYTE.EI..E...KPR.LWALYFNMRDS
RetrocopyRVTELCSSTMTCMKDTYLVHLTCSSSKTAREDLESVVKKLFTPYTETEINEEELTKPRLLWALYFNMRDS
ParentalSDISRSCYNDLPSNVYVCSGPDCGLGNDNAVKQAETLFQEICPNEDFCPPPPNPEDIILDGDSLQPEASE
S.ISRS.YN.LPSNVYVCSGPDCGLGN..AVKQAETLFQEI.P.E.FCPPPPNPED.I.DGD..QPE...
RetrocopySGISRSLYNGLPSNVYVCSGPDCGLGNEHAVKQAETLFQEIFPTEEFCPPPPNPEDVIFDGDDKQPETPG
ParentalSSAILEANSETFKESTNLGNLEE
......A..E...ES.NL...E.
RetrocopyTNNVVMAKLESSEESKNLESPEK

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_prefrontal_cortex 3 .95 RPM 20 .32 RPM
SRP007412_cerebellum 3 .66 RPM 28 .75 RPM
SRP007412_heart 5 .80 RPM 10 .58 RPM
SRP007412_kidney 3 .61 RPM 18 .80 RPM
SRP007412_liver 1 .77 RPM 4 .98 RPM
SRP007412_testis 13 .49 RPM 3 .79 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_400 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_400 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_400 has 10 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_56
Gorilla gorilla retro_ggor_488
Pongo abelii retro_pabe_215
Macaca mulatta retro_mmul_460
Mus musculus retro_mmus_284
Rattus norvegicus retro_rnor_981
Oryctolagus cuniculus retro_ocun_893
Bos taurus retro_btau_227
Canis familiaris retro_cfam_1873
Equus caballus retro_ecab_36
Parental genes homology:
Parental genes homology involve 21 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000101901 retrocopy
retro_amel_733,
Bos taurus ENSBTAG000000095981 retrocopy
retro_btau_227,
Canis familiaris ENSCAFG000000174061 retrocopy
retro_cfam_1873,
Equus caballus ENSECAG000000192011 retrocopy
retro_ecab_36,
Felis catus ENSFCAG000000306521 retrocopy
retro_fcat_1744,
Homo sapiens ENSG000001884191 retrocopy
retro_hsap_56,
Gorilla gorilla ENSGGOG000000229121 retrocopy
retro_ggor_488,
Loxodonta africana ENSLAFG000000005231 retrocopy
retro_lafr_441,
Myotis lucifugus ENSMLUG000000112861 retrocopy
retro_mluc_138,
Macaca mulatta ENSMMUG000000167761 retrocopy
retro_mmul_460,
Monodelphis domestica ENSMODG000000143641 retrocopy
retro_mdom_1776,
Mustela putorius furoENSMPUG000000011941 retrocopy
retro_mputfur_831,
Mus musculus ENSMUSG000000255311 retrocopy
retro_mmus_284,
Nomascus leucogenys ENSNLEG000000027621 retrocopy
retro_nleu_120,
Oryctolagus cuniculus ENSOCUG000000128191 retrocopy
retro_ocun_893,
Pongo abelii ENSPPYG000000205201 retrocopy
retro_pabe_215,
Pan troglodytes ENSPTRG00000022071 1 retrocopy
retro_ptro_400 ,
Rattus norvegicus ENSRNOG000000001611 retrocopy
retro_rnor_981,
Sarcophilus harrisii ENSSHAG000000175681 retrocopy
retro_shar_127,
Ictidomys tridecemlineatus ENSSTOG000000221111 retrocopy
retro_itri_870,
Vicugna pacos ENSVPAG000000019631 retrocopy
retro_vpac_231,


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