RetrogeneDB ID:

retro_itri_870

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393336.1:8838128..8840054(+)
Located in intron of:ENSSTOG00000012707
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CHM
Ensembl ID:ENSSTOG00000022111
Aliases:None
Description:choroideremia (Rab escort protein 1) [Source:HGNC Symbol;Acc:1940]


Retrocopy-Parental alignment summary:






>retro_itri_870
ATGGCAGACATTCTCCCCACAGAGTTTGATGTGATTATAATAGGAACAGGTCTGCCTGAATCCATCCTTGCTGCTGCATG
CTCAAGAAGTGGACAGAGGGTTCTACATATTGATTCAAGAAGCTACTATGGAGGGAATTGGGCTAGTTTCAGTTTTTCAG
GATTGCTATCCTGGTTGCAGGAGTATCAGCAAAACAGAGATACTGAGGAAGAAAATACTGCCTGGGAAGACTTGATTCAT
GAAACAGAGGAAGGCATCACTCTTTGCAAGAAGGATGAAACCATTCAACACATAGAAGTTTTTTGCTATGCCAGTCAAGA
TAAAGAGCACAATGTTCAAGAGATCGGTGCTCTTCAGAAAAGTCCCTCCTCAATGACATCTAGTACCCTCATTGAATCTG
TGGATTCTGCGTGCTTGCCCAAAGAAAGGGACTCCTCATACTTCACTAGCTCTGAAATATCTGCCCAACATACCCAAAAA
AGTGATAAAGATATTTCACTAGAAGTAACTGATATACAAGAATCATTAGAGAAAGATAAAACTTGTATACACACAATTTC
AGGTGGGAGTAAAGGTGAAAACAAACCTACAATAGAAGATAACATTGATCAGCCAAAGAGAAATAGGATTACTTATCCTC
TAATAGTTGAAGAAGGCAGGAGATTTAATATTGATTTGGTATCAAAGCTGCTATATTCCCAAGGATCACTGATTGATCTT
TTAATCAAATCAAATGTTAGTCGTTATGCAGAATTTAAAAATGTAACTAGGATTCTTGCATTTCGGGAAGGAAAGGTAGA
ACAGGTGCCTTGCTCCAGAGCAGATGTGTTTAATAGCAAAGAACTCACTATGGTTGAAAAAAGGATGCTGATGAAATTTC
TTACCTTTTGTTTAGACTATGAACAACAACCTGATGAATACCAAGATTTCAAGCAATGTTCATTTTCAGAGTTCTTAAAA
ACTAAAAAGTTAACCCCCAGCCTCCAACACTTTATACTACACTCAATTGCAATGACATCAGAATCATCATGTAGCACATT
AGATGGCCTTAAAGCAACAAAAAACTTCCTTCAGTGTCTTGGACGGTTTGGCAACACTCCGTTTTTATTTCCCTTATATG
GCCAAGGAGAAATTCCCCAGTGTTTTTGCAGGATGTGTGCTGTTTTTGGTGGAATCTATTGTCTTCGCCATAAAGTACAA
TGCCTTGTAGTTGACAAAGAATCTGGTAGATGTAAAGCAATTGTAGATCACTTGGGTCAAAGAATAAATGCTAAATATTT
TATTGTGGAGGATAGTTACCTTTCTCAGGAAACATGCTCCAATGTGCAGTATAAACAGATCTCAAGGGCAATACTCATTA
CAGATCAGTCTGTACTAAAGACAGAGTCAGATCAACAGATTTCCATTTTGATAGTGCCTCCAATGGAATCAGGAACCTGT
TCTGTTCGGGTCACGGAATTATGTTCATCAACCATGACATGCATGAAAGACACGTATCTAGTACATCTGACCTGTGCATC
TTCAAAAACAGCAAGAGAAGACTTAGAATCCGTGGTGAAGAAATTATTCACTCCTTTTACTGAAACAAAAGAAGAAAAAG
AAGAACTTAGAAAGCCAAGACTTTTGTGGGCTCTATATTTTAATATGAGAGATTCCTCGGGAATCAGCAGAAGCTCCTAT
GATGGCTTACCTTCAAATGTTTATGTCTGCTCTGGGCCTGACTGTGGACTGGGAAATGAGCATGCAGTCAAACAAGCAGA
AACTCTGTTTCAGGAGATGTTTCCTGGTGAAGAATTCTGTCCTCCTCCTCCAAATCCAGAAGACATTATCTTTGATGGTG
ATGATAAGCAACCAGAAGCTCCTGGAACCAACGTAATAATGGCCAAGCTTGAATCCCCCGAGGAAAGCCAAAACTTGGAA
AGCCCG

ORF - retro_itri_870 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.3 %
Parental protein coverage: 99.23 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMADNLPSEFDVIVIGTGLPESIIAAACSRSGQRVLHVDSRNYYGGNWASFSFSGLLSWLKEYQENNDIVI
MAD.LP.EFDVI.IGTGLPESI.AAACSRSGQRVLH.DSR.YYGGNWASFSFSGLLSWL.EYQ.N.D...
RetrocopyMADILPTEFDVIIIGTGLPESILAAACSRSGQRVLHIDSRSYYGGNWASFSFSGLLSWLQEYQQNRDTEE
ParentalDNSLWQEQILENEEAIALSRKDKTIQHVEVFCYASQDLHEYVEEAGALKKNHACVTPVNSSKAADSACLP
.N..W...I.E.EE.I.L..KD.TIQH.EVFCYASQD....V.E.GAL.K.....T........DSACLP
RetrocopyENTAWEDLIHETEEGITLCKKDETIQHIEVFCYASQDKEHNVQEIGALQKSPSSMTSSTLIESVDSACLP
ParentalTEDASLSTESCEVPAEQTPSSDPESTLEVNDAEATGEKENHSDDKISEEKTNENVPTAEDTAEQPKKNRI
.E..S....S.E..A..T..SD....LEV.D.....EK.......IS.....EN.PT.ED...QPK.NRI
RetrocopyKERDSSYFTSSEISAQHTQKSDKDISLEVTDIQESLEKDKTCIHTISGGSKGENKPTIEDNIDQPKRNRI
ParentalTYSQIVKEGRRFNIDLVSKLLYSRGMLIDLLIKSNVSRYAEFKNITRILAFREGRMEQVPCSRADVFNSK
TY..IV.EGRRFNIDLVSKLLYS.G.LIDLLIKSNVSRYAEFKN.TRILAFREG..EQVPCSRADVFNSK
RetrocopyTYPLIVEEGRRFNIDLVSKLLYSQGSLIDLLIKSNVSRYAEFKNVTRILAFREGKVEQVPCSRADVFNSK
ParentalQLTMVEKRMLMKFLTFCMEYEEHPDEYKAYEDITFSEFLKTQKLTPNLQYFVLHSIAMTSETTSSTIDGL
.LTMVEKRMLMKFLTFC..YE..PDEY.......FSEFLKT.KLTP.LQ.F.LHSIAMTSE...ST.DGL
RetrocopyELTMVEKRMLMKFLTFCLDYEQQPDEYQDFKQCSFSEFLKTKKLTPSLQHFILHSIAMTSESSCSTLDGL
ParentalKATKNFLHCLGRYGNTPFLFPLYGQGELPQCFCRMCAVFGGIYCLRHSVQCLVVDKESRKCKAIIDQFGQ
KATKNFL.CLGR.GNTPFLFPLYGQGE.PQCFCRMCAVFGGIYCLRH.VQCLVVDKES..CKAI.D..GQ
RetrocopyKATKNFLQCLGRFGNTPFLFPLYGQGEIPQCFCRMCAVFGGIYCLRHKVQCLVVDKESGRCKAIVDHLGQ
ParentalRIISKHFLVEDSYFSENTCSRVQYRQISRAVLITDRSVLKSDSDQQISILIVPAEEPGSFSVRVIELCSS
RI..K.F.VEDSY.S..TCS.VQY.QISRA.LITD.SVLK..SDQQISILIVP..E.G..SVRV.ELCSS
RetrocopyRINAKYFIVEDSYLSQETCSNVQYKQISRAILITDQSVLKTESDQQISILIVPPMESGTCSVRVTELCSS
ParentalTMTCMKGTYLVHLTCTSSKTAREDLEAVVEKLFTPYTETGIENEEVEKPRILWALYFNMRDSSDINRNCY
TMTCMK.TYLVHLTC.SSKTAREDLE.VV.KLFTP.TET..E.EE..KPR.LWALYFNMRDSS.I.R..Y
RetrocopyTMTCMKDTYLVHLTCASSKTAREDLESVVKKLFTPFTETKEEKEELRKPRLLWALYFNMRDSSGISRSSY
ParentalNDLPSNVYVCSGPDGGLGNDNAVKQAEIIFQSICPNEDFCPPPPNPEDIVLDGDSSQPESSESSAILEAN
..LPSNVYVCSGPD.GLGN..AVKQAE..FQ...P.E.FCPPPPNPEDI..DGD..QPE......I..A.
RetrocopyDGLPSNVYVCSGPDCGLGNEHAVKQAETLFQEMFPGEEFCPPPPNPEDIIFDGDDKQPEAPGTNVIM-AK
ParentalSETPAESTTLGNP
.E.P.ES..L..P
RetrocopyLESPEESQNLESP

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






RNA-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_itri_870 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_870 was not experimentally validated.

Retrocopy orthology:
Ictidomys tridecemlineatus 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 22 parental genes, and 22 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 ENSPTRG000000220711 retrocopy
retro_ptro_400,
Rattus norvegicus ENSRNOG000000001611 retrocopy
retro_rnor_981,
Sarcophilus harrisii ENSSHAG000000175681 retrocopy
retro_shar_127,
Ictidomys tridecemlineatus ENSSTOG000000064491 retrocopy
retro_itri_757,
Ictidomys tridecemlineatus ENSSTOG00000022111 1 retrocopy
retro_itri_870 ,
Vicugna pacos ENSVPAG000000019631 retrocopy
retro_vpac_231,


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