RetrogeneDB ID:

retro_amel_733

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL192597.1:480395..482219(+)
Located in intron of:ENSAMEG00000013961
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CHM
Ensembl ID:ENSAMEG00000010190
Aliases:None
Description:choroideremia (Rab escort protein 1) [Source:HGNC Symbol;Acc:1940]


Retrocopy-Parental alignment summary:






>retro_amel_733
AGAAGTTACTATGGAGGAAACTGGGCAAGTTTCAGCTTTTCGGGATTGCTCTCCTGGTTGAAGGAGTGTCAGCAAGACAG
TGACGTTGTGGAAGAAAGCACTGGCTCATGGCAAGACCTGATCCATGACACGGAGGAAGCTATCACTCTTCGCACGAAGG
ACGGAAGCATTCGACACACAGAAGTTTTTTGTTATGCCGGTCAGGATACAGATGACAATACGGAAGAGGTTGATGCTGTG
CAGAAAAACCCTTCCTCAGTAACATCTAGTACCTCCACTGACCCTCTGGGTTCTGCATGCTTGTCTGAAGAAACACACTC
GTCTGCTACTAGCCATGAGATGCCTGCCAAAGACACTCCAAAAAGTGACGGAGAAGTTTCACTAGAAGTAACTGATGCCG
AGGACACCTTGGCAAAAGAAAAACATTGTGGAGACGAAACTTGGACACACACAGTTTCAGAGGGAGTTAAAGATGAAAAC
AAGCCTGTAGAGGAAGACAACACTGACCAACCAAAGAGAAATAGAGTTACTTACTCTCAAATAGTTAAAGAAGGCAGGAG
GTTTAATATTGATTTGGTATCAAAACTGCTGTATTCTCAAGGATTGCTAATTGATCTCTTAATCAAATCAAATGTTAGTC
GTTACGCAGAATTTAAAAACGTCACTAGGATTCTTGCATTTCGTGAAGGAAAAGTAGAACAGGTGCCTTGTTCCAGAGCA
GATGTCTTTAATAGCAAGGAACTCACTATGGTTGAAAAGAGGATACTGATGAAATTTCTTACGTTTTGTTTAGACTACGA
ACAACATCCTGATCAATACCAAGCTTTTGTGCAGTGCTCATTTTCGGAGTACTTACAGACTAAAAAATTAACCCCCAATC
TCCAACATTTTGTGCTGCACTCAATTGCAATGACAGAGTCATCTTGCAGTACAATAGATGGCCTTAAAGCAACTAAAAAC
TTCCTTCGGTGTCTTGGACGATTTGGCAACACTCCCTTTTTATTTCCCTTGTATGGGCAAGGAGAAATTCCCCAGTGTTT
CTGCAGGATGTGTGCAGTTTTTGGTGGAATCTATTGTCTTCGTCATAAAGTTCAATGCCTTGTAGTTGACAAAGAATCTG
GAAGATGTAAAGCAATTATAGATCACTTAGGTCAAAGAATAAGTGCTAAATATTTTATTGTGGAAGATAGTTACCTTTCT
GAGGAAACATGCTCAAATGTGCAGTATAAGCAGATCTCCAGGGCAGTGCTCATTACAGATCAGTCTATACTAAAGGCAGA
TTCAGATCAGCAAATTTCCATCTTGGTGGTGCCTCCAGTGGAATCGGGAACGTGTGCTGTTCGTGTCACTGAATTATGTT
CTTCAACCATGACGTGCATGAAAGACACTTATCTGGTACACCTGACTTGTTCATCTTCGAAAACAGCCAGAGAAGACTTG
GAGTCAGTCGTGAAGAAATTATTCACCCCATATACTGAAACTGAAATAGACAAGGAAGAACTTACAAAGCCCAGACTCTT
GTGGGCTCTTTATTTTAATATGAGAGATTCCTCGGAAATCAGCCGAAGCTCCTACAATGGCTTGCCTTCCAATGTCTATG
TCTGCTCCGGGCCTGACTGCGGACTGGGAAGTGAGCATGCTGTCAAGCAAGCCGAAACGCTGTTCCAGGAGATCTTTCCC
AATGAAGAGTTCTGCCCCCCACCTCCAAATCCAGAAGACATTATCTTTGATGGTGATGATAAGCAACCAGAGGCTCCTGG
AACCAATAATATAATCATGGCCAAAGTAGACTCCTCTGAGGGAAGGAGAAACCTAGAAAGCCCG

ORF - retro_amel_733 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.66 %
Parental protein coverage: 98.23 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalRNYYGGNWASFSFSGILSWLKEYQENSDIVNESP-TWQEQILENEEAIALSRKDKTIQHVEVFCYASQDL
R.YYGGNWASFSFSG.LSWLKE.Q..SD.V.ES...WQ..I...EEAI.L..KD..I.H.EVFCYA.QD.
RetrocopyRSYYGGNWASFSFSGLLSWLKECQQDSDVVEESTGSWQDLIHDTEEAITLRTKDGSIRHTEVFCYAGQDT
ParentalHEDVEEAGALQKNHASVISGNPTEAAHSAYQPSEDESLCTVSCEMPTEQTPSSDQETALEINDVEVTGEK
....EE..A.QKN..SV.S...T....SA....E..S..T.S.EMP...TP.SD.E..LE..D.E.T..K
RetrocopyDDNTEEVDAVQKNPSSVTSSTSTDPLGSACLSEETHSSAT-SHEMPAKDTPKSDGEVSLEVTDAEDTLAK
ParentalEKRYDDKTHAKSASEEETSENVPIAEDTVLQPKKNRITYSQIIKEGRRFNIDLVSKLLYSRGLLIDLLIK
EK...D.T.....SE....EN.P..ED...QPK.NR.TYSQI.KEGRRFNIDLVSKLLYS.GLLIDLLIK
RetrocopyEKHCGDETWTHTVSEGVKDENKPVEEDNTDQPKRNRVTYSQIVKEGRRFNIDLVSKLLYSQGLLIDLLIK
ParentalSNVSRYAEFKNITRILAFREGRVEQVPCSRADVFNSKQLTMVEKRMLMKFLTFCMEYEKHPDEYKAYEEI
SNVSRYAEFKN.TRILAFREG.VEQVPCSRADVFNSK.LTMVEKR.LMKFLTFC..YE.HPD.Y.A....
RetrocopySNVSRYAEFKNVTRILAFREGKVEQVPCSRADVFNSKELTMVEKRILMKFLTFCLDYEQHPDQYQAFVQC
ParentalTFSEYLKTQKLTPNLQYFVLHSIAMTSETASNTVDGLKATKNFLHCLGRYGNTPFLFPLYGQGELPQCFC
.FSEYL.T.KLTPNLQ.FVLHSIAMT.E....T.DGLKATKNFL.CLGR.GNTPFLFPLYGQGE.PQCFC
RetrocopySFSEYLQTKKLTPNLQHFVLHSIAMT-ESSCSTIDGLKATKNFLRCLGRFGNTPFLFPLYGQGEIPQCFC
ParentalRMCAVFGGIYCLRHSVQCLVVDKESRKCKAIIDQFGQRIISKHFLVEDSYFSENTCSHVQYRQISRSVLI
RMCAVFGGIYCLRH.VQCLVVDKES..CKAIID..GQRI..K.F.VEDSY.SE.TCS.VQY.QISR.VLI
RetrocopyRMCAVFGGIYCLRHKVQCLVVDKESGRCKAIIDHLGQRISAKYFIVEDSYLSEETCSNVQYKQISRAVLI
ParentalTDRSVLKTDSDQQISILTVPGEEPGTFAVRVIELCPSTMTCMKGTYLVHLTCTSSKTAREDLEPVVQKLF
TD.S.LK.DSDQQISIL.VP..E.GT.AVRV.ELC.STMTCMK.TYLVHLTC.SSKTAREDLE.VV.KLF
RetrocopyTDQSILKADSDQQISILVVPPVESGTCAVRVTELCSSTMTCMKDTYLVHLTCSSSKTAREDLESVVKKLF
ParentalTPYTETEIENEEVEKPRLLWALYFNMRDSSDISRNSYNDLPSNVYVCSGPDCGLGNDNAVKQAERLFQLI
TPYTETEI..EE..KPRLLWALYFNMRDSS.ISR.SYN.LPSNVYVCSGPDCGLG...AVKQAE.LFQ.I
RetrocopyTPYTETEIDKEELTKPRLLWALYFNMRDSSEISRSSYNGLPSNVYVCSGPDCGLGSEHAVKQAETLFQEI
ParentalCPNEDFCPPPPNPEDIIIDGDSLQSETSEFSVIPEANSETPKESTSLGNP
.PNE.FCPPPPNPEDII.DGD..Q.E......I..A..........L..P
RetrocopyFPNEEFCPPPPNPEDIIFDGDDKQPEAPGTNNIIMAKVDSSEGRRNLESP

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_amel_733 retrocopy.

TSS - click to see more details

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab - click to see more details

retro_amel_733 was not experimentally validated.

Retrocopy orthology:
Ailuropoda melanoleuca does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 21 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG00000010190 1 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 ENSPTRG000000220711 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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