RetrogeneDB ID:

retro_btau_189

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:X:98345057..98346008(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000046659
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:FOXR1
Ensembl ID:ENSBTAG00000014606
Aliases:LOC788135, FOXR1
Description:None


Retrocopy-Parental alignment summary:






>retro_btau_189
ATGGACTTAAAACTAAAAAATCCTGAGTTCTGGTACAGTTTCCATGGCCAGATCCCAGGGCTGCTGGACTGGGACATGGG
AAATGAGTTCTTCCTTCCTTGCACCACAGACCAGTGCCCCTTAGCTGAGCAGAACCTTGCCAAATACAGACTTCAAGTAA
TGGAGACTCCAAAAGTACCTCAAGAGAGGGGATCCAGTCCTGGAAAAGATCGTCCTAACTCTGAACCCAATCTGTGGATG
TGGGTGAATCCCAACATCGCATGCTCCCTTGGCAGCCAGGAGACCCCAGAGCCCAGTAAGAAAAAGGATCTGGCACACAT
ACTTCTTTCTCCTCAGCTACTCGCAAAAGATGAAGTACCTAACTGCTCAGAGGCCACAGTGATGCAGTCCCTGCCATCTT
CCTCCAGCAAGCAATCTCCCCTACAGAAGCAGATCACCTCTTTTTCCAGTGACAGGGAGCTTACAGAAGATGAGACCAAG
GAAAAAGATAGCAACTCCTCTGTGGCCCTCCAGTCCCCAAACAAAGGGGAGTGCTTCCAGAGCCAGAACCTATGGCAAGG
CAACAGCCAGGAGAGGAAGTCCTGGCCTCGTCCCCCCCTCAATTACAGTCACCTAATTGCTCTGGCACTTAGAAACAGCC
CTCCCTGTGGCCTCAATGTGCAAGAGATCTACAGTTTCACCCAACAGCATTTCCCCTTTTTCTGGACAGCTCCATATGGA
TGGAAGAATACCATCCGCCACAACCTCTGCTTCCTGGACAGCTTTGAGAAGGCGCCAGTCAGTCTTCAGGATGGGGCCAG
TGCAAGGCCAAGGCCTGGCCTCTGGAGGCTTACTGAGGAGGGACACCGCCGCTTTCAGGAGGAGACTCGTGCCTTAGCCT
CTGCTAGAAGAGAGAGTATTCAACAGTGCATGAGCCATCCAGATGTTATGACTTCCCTCTTTGACCTTTGA

ORF - retro_btau_189 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 60.44 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVDLKLQHVDFWASLHGQVPGLLDWDMGNESFLAFATSHLPLAEQNLARYKLRIVEPPMLPLEKKPNPDKD
.DLKL....FW.S.HGQ.PGLLDWDMGNE.FL...T...PLAEQNLA.Y.L...E.P..P.E....P.KD
RetrocopyMDLKLKNPEFWYSFHGQIPGLLDWDMGNEFFLPCTTDQCPLAEQNLAKYRLQVMETPKVPQERGSSPGKD
ParentalGPDFEPNLWMWVDPNIMFPPGKLEVPEPSKGKNLTTTAPSPQPVPKEDFAKCPEATEVELLSPPGDQCSP
.P..EPNLWMWV.PNI....G..E.PEPSK.K.L.....SPQ...K.....C.EAT....L.......SP
RetrocopyRPNSEPNLWMWVNPNIACSLGSQETPEPSKKKDLAHILLSPQLLAKDEVPNCSEATVMQSLPSSSSKQSP
ParentalWKRFATSLSNWELTEEKEAEDQDDRSSVALPSSHKPAPLQSRRLRQANSQEGRLWSRPPLNYFHLIALAL
.....TS.S......E.E....D..SSVAL.S..K....QS..L.Q.NSQE...W.RPPLNY.HLIALAL
RetrocopyLQKQITSFSSDRELTEDETKEKDSNSSVALQSPNKGECFQSQNLWQGNSQERKSWPRPPLNYSHLIALAL
ParentalRNSAPCGLNVQQIYSFTRQHFPFFRTAPEGWKNTVRHNLCFRDSFEKVPVSMQGGVSSRPRSCLWKLTDE
RNS.PCGLNVQ.IYSFT.QHFPFF.TAP.GWKNT.RHNLCF.DSFEK.PVS.Q.G.S.RPR..LW.LT.E
RetrocopyRNSPPCGLNVQEIYSFTQQHFPFFWTAPYGWKNTIRHNLCFLDSFEKAPVSLQDGASARPRPGLWRLTEE
ParentalGHRRFAEEARALASTRLERIQQCMSQPDVMSSLFDL
GHRRF.EE.RALAS.R.E.IQQCMS.PDVM.SLFDL
RetrocopyGHRRFQEETRALASARRESIQQCMSHPDVMTSLFDL

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
ERP005899_liver 0 .00 RPM 0 .00 RPM
ERP005899_muscle 0 .00 RPM 0 .00 RPM
SRP017611_brain 0 .00 RPM 0 .00 RPM
SRP017611_kidney 0 .00 RPM 0 .00 RPM
SRP017611_liver 0 .00 RPM 0 .00 RPM
SRP030211_testis 0 .45 RPM 0 .66 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_btau_189 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_189 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_189 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_72
Pan troglodytes retro_ptro_94
Pongo abelii retro_pabe_69
Callithrix jacchus retro_cjac_4066
Parental genes homology:
Parental genes homology involve 18 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000000531 retrocopy
retro_amel_39,
Bos taurus ENSBTAG00000014606 1 retrocopy
retro_btau_189 ,
Canis familiaris ENSCAFG000000124171 retrocopy
retro_cfam_209,
Callithrix jacchus ENSCJAG000000136561 retrocopy
retro_cjac_4066,
Dasypus novemcinctus ENSDNOG000000094141 retrocopy
retro_dnov_22,
Dipodomys ordii ENSDORG000000019601 retrocopy
retro_dord_651,
Homo sapiens ENSG000001763021 retrocopy
retro_hsap_72,
Microcebus murinus ENSMICG000000026801 retrocopy
retro_mmur_38,
Macaca mulatta ENSMMUG000000227221 retrocopy
retro_mmul_125,
Mustela putorius furoENSMPUG000000048901 retrocopy
retro_mputfur_161,
Nomascus leucogenys ENSNLEG000000073761 retrocopy
retro_nleu_50,
Otolemur garnettii ENSOGAG000000072581 retrocopy
retro_ogar_296,
Procavia capensis ENSPCAG000000101321 retrocopy
retro_pcap_12,
Pongo abelii ENSPPYG000000039471 retrocopy
retro_pabe_69,
Pan troglodytes ENSPTRG000000043581 retrocopy
retro_ptro_94,
Sorex araneus ENSSARG000000113191 retrocopy
retro_sara_38,
Sus scrofa ENSSSCG000000151011 retrocopy
retro_sscr_36,
Ictidomys tridecemlineatus ENSSTOG000000143211 retrocopy
retro_itri_158,


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