RetrogeneDB ID:

retro_ecab_36

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:30:3057291..3059253(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSECAG00000002924
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:CHM
Ensembl ID:ENSECAG00000019201
Aliases:None
Description:choroideremia (Rab escort protein 1) [Source:HGNC Symbol;Acc:1940]


Retrocopy-Parental alignment summary:






>retro_ecab_36
ATGGCGGACAGTCTCCCGACAGAGTTTGATGTGATTGTAATAGGGACAGGTTTGCCTGAATCCATCCTTGCAGCTGCATG
TTCAAGAAGTGGTCAGAGGGTTTTGCATCTTGATTCAAGAAGTTACTATGGAGGAAACTGGGCTAGTTTCAGCTTTTCAG
CATTGCTGTCCTGGTTGGAGTGTCAGCAAAACAGTGACCCTGGGGAAGAAGGTTCTGCTGCGTGGCAGGACCTGATCCAT
GAAACAGAAGAAGCCATCACCCTTTGCAGCAAGGACAAAACCATTCAGCACACAGAAGTGTTCTGTTATGCCAGTCAGGA
TGTGGATGACAATATTGAAGAGACTGATGCCCTACAGAGAACTCCTTCCTGGGTAGCACCCACTCCCCTCACCAACCCTC
TGGTTCCAGCATGCTTGTCTGAAGAAACACCCTCTTTGTGCGTTACAAGGCATGAGATGCCTGCCAAAGACACTCCAGAA
AACGATGGAGAGATTTCGCCAGAAGTCACAGATGTAGAGGAAACCCTGGCGAAAGAAAATAATCGTGGAGATAAAACTTG
TACACACGCAGTTTCAGATGGAGCTAAAGATGAAAACAAACCTATAGTGGAAGATAGCACTGATCAACCAAAGAGAAATA
GGATTACTTACTCTCAAATAGTTAAAGAAGGCAGGAGGTTTAATATTGATTTGGTATCAAAGCTACTATATTCTCAAGGA
TTGCTAATTGACCTTTTAATCAAATCAAATGTTAGTCGTTATGCAGAATTTAAAAATGTCACTAGGATTCTTGCATTTCG
GGAAGGAAAAGTAGAACAGGTGCCTTGTTCCAGAGCAGATGTCTTTAACAGCAAAGCACTCACCATGGTTGAAAAGAGGA
TGCTAATGAAATTTCTTACATTTTGTTTAGACTATGAACAACATCCTGAGGAATACCAAGCTTTCATGCAATGCTCTTTT
TCAGAGTACTTAAAAACTAAAAAATTAACCCCCAACCTCCAACATTTTGTACTGCACTCAATTGCAATGACAGAGTCGTC
TTGCACTACAATAGATGGCCTTAAAGCAACAAAAAACTTCCTTCAGTGTCTTGGCCGATTTGGCAACACCCCCTTTTTAT
TCCCCTTGTATGGCCAAGGAGAAGTTCCCCAGTGTTTCTGCAGGATGTGTGCAGTTTTTGGTGGAATCTATTGTCTTCGC
CATAAAATACAATGCCTTGTAGTTGACAAAGAATCCGGAAGATGTCAAGCAATCATAGATCACTTTGGCCAAAGAATAAA
TGCTAAATATTTTATTGTGGAGGACAGTTACCTTTCTGAGGACACGTGCTCAAATGTGCAGTATAAACAGATCTCCAGGG
CAGTGCTCATTACGGATCAGTCTGTACTAAAGACAGATTCAGATCAGCAGATTTCCATTTTGATAGTGCCTCCGGCGGAA
CCAGGAATGTGTGCTGTTCGGGTCACTGAACTATGTTCTTCAACGATGACATGCATGAAAGACACTTATCTGGTACATCT
GACCTGTTCGTCCTCTAAAACAGCAAGAGAAGACTTAGAATCAGTGGTGAGGAAATTATTCATTCCATATGCTGAAACAG
AAACAGACAGGGAAGGACTTAGAAAGCCAAGACTCTTGTGGGCTCTTTATTTTAATATGAGGGATTCCTCAGAAATCAGC
AGAAGCTCCTATAATGGCTTACCTTCCAATGTTTATGTCTGCTCTGGGCCTGACTGTGGACTAGGAAATGAGCACGCAGT
CAGGCAAGCTCAAACGCTTTTCCAGGAGATCTTTCCAACTGAAGAATTCTGCCCTCCACCTCCTAATCCAGAAGACATTA
TCTTTGACGGTGATGACAAGCAGCCAGAGGTTCCTGGAACCACTAATAGAATAATTGCCAAACTAGAATCTTCTGAGGAT
TGCAAAAACCTAGAAAACCATGAGAACCACCTTCAAAATTAG

ORF - retro_ecab_36 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.46 %
Parental protein coverage: 99.39 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMADNLPSEFDVIVIGTGLPESIIAAACSRSGQRVLHVDSRSYYGGNWASFSFSGLLSWLKEYQENSDIVN
MAD.LP.EFDVIVIGTGLPESI.AAACSRSGQRVLH.DSRSYYGGNWASFSFS.LLSWL.E.Q.NSD...
RetrocopyMADSLPTEFDVIVIGTGLPESILAAACSRSGQRVLHLDSRSYYGGNWASFSFSALLSWL-ECQQNSDPGE
ParentalE-SPAWQEQILENEEAIALSRKDKTIQHVEVFCYASQDLHEDVEEAGALQKNHAAVTSANSTEAADSACL
E.S.AWQ..I.E.EEAI.L..KDKTIQH.EVFCYASQD.....EE..ALQ.....V.....T.....ACL
RetrocopyEGSAAWQDLIHETEEAITLCSKDKTIQHTEVFCYASQDVDDNIEETDALQRTPSWVAPTPLTNPLVPACL
ParentalPTEDESLSTASCERPAEQTPSSDAESALEVNDAEATGEKENHCDDKTCVPSTSEEETGENVPTVEDTAEQ
..E..SL.....E.PA..TP..D.E...EV.D.E.T..KEN...DKTC....S.....EN.P.VED...Q
RetrocopySEETPSLCVTRHEMPAKDTPENDGEISPEVTDVEETLAKENNRGDKTCTHAVSDGAKDENKPIVEDSTDQ
ParentalPKKNRITYAQIIKEGRRFNIDLVSKLLYSRGLLIDLLIKSNVSRYAEFKNITRILAFREGRVEQVPCSRA
PK.NRITY.QI.KEGRRFNIDLVSKLLYS.GLLIDLLIKSNVSRYAEFKN.TRILAFREG.VEQVPCSRA
RetrocopyPKRNRITYSQIVKEGRRFNIDLVSKLLYSQGLLIDLLIKSNVSRYAEFKNVTRILAFREGKVEQVPCSRA
ParentalDVFNSKQLTMVEKRMLMKFLTFCMEYEEHPDEYKAYEEITFSEYLKTQKLTPNLQYFVLHSIAMTSETAS
DVFNSK.LTMVEKRMLMKFLTFC..YE.HP.EY.A.....FSEYLKT.KLTPNLQ.FVLHSIAMT.E...
RetrocopyDVFNSKALTMVEKRMLMKFLTFCLDYEQHPEEYQAFMQCSFSEYLKTKKLTPNLQHFVLHSIAMT-ESSC
ParentalSTIDGLKATKNFLHCLGRYGNTPFLFPLYGQGELPQCFCRMCAVFGGIYCLRHSVQCLVVDKESRKCKAI
.TIDGLKATKNFL.CLGR.GNTPFLFPLYGQGE.PQCFCRMCAVFGGIYCLRH..QCLVVDKES..C.AI
RetrocopyTTIDGLKATKNFLQCLGRFGNTPFLFPLYGQGEVPQCFCRMCAVFGGIYCLRHKIQCLVVDKESGRCQAI
ParentalIDQFGQRIISKHFLVEDSYFSENTCSHVRYRQISRAVLITDRSVLKTDSDQQISILTVPAEEPGTFAVRV
ID.FGQRI..K.F.VEDSY.SE.TCS.V.Y.QISRAVLITD.SVLKTDSDQQISIL.VP..EPG..AVRV
RetrocopyIDHFGQRINAKYFIVEDSYLSEDTCSNVQYKQISRAVLITDQSVLKTDSDQQISILIVPPAEPGMCAVRV
ParentalIELCSSTMTCMKGTYLVHLTCTSSKTAREDLEPVVQKLFTPYTETEIENEEVEKPRLLWALYFNMRDSSD
.ELCSSTMTCMK.TYLVHLTC.SSKTAREDLE.VV.KLF.PY.ETE...E...KPRLLWALYFNMRDSS.
RetrocopyTELCSSTMTCMKDTYLVHLTCSSSKTAREDLESVVRKLFIPYAETETDREGLRKPRLLWALYFNMRDSSE
ParentalISRSSYNDLPSNVYVCSGPDCSLGSDNAVKQAETLFHQICPNEDFCPPPPNPEDIILDGDSVQPEASESS
ISRSSYN.LPSNVYVCSGPDC.LG...AV.QA.TLF..I.P.E.FCPPPPNPEDII.DGD..QPE.....
RetrocopyISRSSYNGLPSNVYVCSGPDCGLGNEHAVRQAQTLFQEIFPTEEFCPPPPNPEDIIFDGDDKQPEVPGTT
ParentalAIPEANSETPRESANLGNPE
....A..E......NL.N.E
RetrocopyNRIIAKLESSEDCKNLENHE

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
SRP021940_articular_cartilage 2 .83 RPM 3 .36 RPM
SRP021940_cerebellum 1 .45 RPM 10 .39 RPM
SRP021940_embryo 21 .40 RPM 13 .37 RPM
SRP021940_placental_villous 2 .07 RPM 6 .35 RPM
SRP021940_synovial_membrane 2 .91 RPM 5 .90 RPM
SRP021940_testis 0 .58 RPM 0 .83 RPM

ChIP-Seq - click to see more details

Equus caballus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ecab_36 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_36 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_36 has 10 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_56
Pan troglodytes retro_ptro_400
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
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 ENSECAG00000019201 1 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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