RetrogeneDB ID:

retro_cfam_370

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:10:29792..31550(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCAFG00000000049
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RAP1GDS1
Ensembl ID:ENSCAFG00000010267
Aliases:None
Description:RAP1, GTP-GDP dissociation stimulator 1 [Source:HGNC Symbol;Acc:9859]


Retrocopy-Parental alignment summary:






>retro_cfam_370
GCAGATACTCTCAGTGATACCTTGAAGAAGTTGAAGATAACAGCTGTTGACAGAACCGAAGATAGTTTAGAAGGATGCTT
GGATTGTCTGCTTCAAGCCCTGGCTCAAAATAATATGGAAACGAGTGAAAAAAATCCAAGGAAGTGGAATACTTCAGCTG
TTTGTAAGTCTGTTGATTCCACAGTCTTCCTGCACAGCCAAAGTAGCTAATGTCATAGCAGAAGTAGCCAAAAATGAATG
TATGCGTATTCCATGTATGGATACTGGATTGACTTCACCATTGGTGCAGCTGCTAAATAGCAAAGACCAGGAAGTGCTAC
TTCAAATGGGCAGGGCTCTGGGAAGCATATGTTACGATAGCCATGAGGGCAGAAGTGCAGTTGATCAAGCAGGTGGTGCA
CAGATTGTAATTGACCATTTAAGGTCACTATGCAGTATAACAGATCCCACCAATGAAAAGCTCTTGACTGTCTTTTGTGG
TATGCTGATGAACTACAGCAATGAGAAAGATTCCCTTCAAGCTCAGCTTATCAATATGGGTGTTATACCTACCGCAGTGA
AATTACTGGGCATCCATTGCCAAAATGCAGCTCATACAGAAATGTGTCTTGTTGCATTTGGTAACTTAGCAGAACTTGAG
TCAAGTAAAGAACAGTTTGCCAGTACGAACGTTGCTGAAGAGCTAGTAAAACTCTTTAAGAAACAAATAGAACATGATAA
AAAGGAAATTATTTTGGAAGTTCTTTCTCTACTGGCAGAAAATGATGCTATTAAACTACATCTGGTTGAAGCAGGCCTGG
TAGAGTGTCTACTACAGATTGTTCAGCAGAAAGTGGATAGTGACAAAGGGCATGATATTGCTGAGCTCAAAACCGCTTCA
GATCTAATGGTTTTTCTACTTCTTGGATTTGAATCCATGCAGAAATTATTTGAAGAAGGAAAAGGTAATGTGTTTCAAAG
GGTGCTGTCCTGGATTCCATTAAATAACCACCAGCTACAGCTTGCTGGAGCATTGGCAATTGCAAATTTTGCCAGAAACG
GTGGAAACTGTATCCACATGGTAGACAATGGAATTGTAGAAAAACTTATGGATTTACTGGACAGACATGTAGAAGATGGG
AATGTAACTGTACAGCATGCAGCATTAATGACCTCAGAAATCTCGCCATTCCAGTTGTAAAAAAAGCAAAGATGTTATCA
GCTGGAGTCACAGAGGCAGTTTTGAAATTCCTTAAGTCTGAAATGCCTCCAATTCAGTTCAAACTTTTGGGAACCTTAAG
AATGTTAATAGATGCACAAGCAGAAGCTGCTGAACAACTGGGAAAGAATGTTAAATTAGTGGAGCGTTTGGTAGAATGGT
GCAAAGCCAAAGATCATGCTGGTGTGATGGGGGAGTCCAACAGACTGCTGTCTGCCCTCATTCATCACAATAAATCAAAA
GATGTAATTAAAACCATTGTACAGAGTGGTGGCACCAAGCATCCTGTTACCATGGCAACTAGTGAACATGTAGTAATGCA
GAATGAAGCCCTTGTTGCTTTGGCACTAATAGCAGCTTTAGAGTTGAGCACTGCTGAGAAAGATCTAGAAAGTGCTAAAC
TTGTACAGAATTCACACAGACTGCTGGAAGATGAAAGAAGTGCTCCGGAAATCAAATATAATTCCACGGTCCTTATTTGT
GCTCTCATGGGATCTGAATCTCTACAAAAGGAAGTACAGGATTTGGCCTTTCTAGAGGTTGTATCTAAACATCGCAGT

ORF - retro_cfam_370 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.82 %
Parental protein coverage: 96.54 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalADNLSDTLKKLKITAVDRTEDSLEGCLDCLLQ-PWLKIDMETSEKIQGSGILQLFASLLIPQSSCTAKVA
AD.LSDTLKKLKITAVDRTEDSLEGCLDCLLQ.PWLKI......KIQGSGILQLF.SLLIPQSSCTAKVA
RetrocopyADTLSDTLKKLKITAVDRTEDSLEGCLDCLLQ>PWLKIIWKRVKKIQGSGILQLFVSLLIPQSSCTAKVA
ParentalNIIAEVAKNEFMRIPCVDAGLISPLVQLLNSKDQEVLLQTGRALGNICYDSHEGRSAVDQAGGAQIVVDH
N.IAEVAKNE.MRIPC.D.GL.SPLVQLLNSKDQEVLLQ.GRALG.ICYDSHEGRSAVDQAGGAQIV.DH
RetrocopyNVIAEVAKNECMRIPCMDTGLTSPLVQLLNSKDQEVLLQMGRALGSICYDSHEGRSAVDQAGGAQIVIDH
ParentalLRSLCSITDPANEKLLTVFCGMLMNYSNENDSLQAQLINMGVIPTLVKLLGIHCQNAALTEMCLVAFGNL
LRSLCSITDP.NEKLLTVFCGMLMNYSNE.DSLQAQLINMGVIPT.VKLLGIHCQNAA.TEMCLVAFGNL
RetrocopyLRSLCSITDPTNEKLLTVFCGMLMNYSNEKDSLQAQLINMGVIPTAVKLLGIHCQNAAHTEMCLVAFGNL
ParentalAELESSKEQFASTNIAEELVKLFKKQIEHDKREMIFEVLAPLAENDAIKLQLVEAGLVECLLEIVQQKVD
AELESSKEQFASTN.AEELVKLFKKQIEHDK.E.I.EVL..LAENDAIKL.LVEAGLVECLL.IVQQKVD
RetrocopyAELESSKEQFASTNVAEELVKLFKKQIEHDKKEIILEVLSLLAENDAIKLHLVEAGLVECLLQIVQQKVD
ParentalSDKEDDIAELKTASDLMVLLLLGDESMQKLFEGGKGNVFQRVLSWIPSNNHQLQLAGALAIANFARNDGN
SDK..DIAELKTASDLMV.LLLG.ESMQKLFE.GKGNVFQRVLSWIP.NNHQLQLAGALAIANFARN.GN
RetrocopySDKGHDIAELKTASDLMVFLLLGFESMQKLFEEGKGNVFQRVLSWIPLNNHQLQLAGALAIANFARNGGN
ParentalCIHMVDNGIVEKLMDLLDRHVEDGNVTVQHAAL-SALRNLAIPVVNKAKMLSAGVTEAVLKFLKSEMPPV
CIHMVDNGIVEKLMDLLDRHVEDGNVTVQHAAL...LRNLAIPVV.KAKMLSAGVTEAVLKFLKSEMPP.
RetrocopyCIHMVDNGIVEKLMDLLDRHVEDGNVTVQHAAL<NDLRNLAIPVVKKAKMLSAGVTEAVLKFLKSEMPPI
ParentalQFKLLGTLRMLIDAQAEAAEQLGKNVKLVERLVEWCEAKDHAGVMGESNRLLSALIRHSKSKDVIKTIVQ
QFKLLGTLRMLIDAQAEAAEQLGKNVKLVERLVEWC.AKDHAGVMGESNRLLSALI.H.KSKDVIKTIVQ
RetrocopyQFKLLGTLRMLIDAQAEAAEQLGKNVKLVERLVEWCKAKDHAGVMGESNRLLSALIHHNKSKDVIKTIVQ
ParentalSGGIKHLVTMATSEHVIMQNEALVALALIAALELGTAEKDLESAKLVQILHRLLEDERSAPEIKYNSMVL
SGG.KH.VTMATSEHV.MQNEALVALALIAALEL.TAEKDLESAKLVQ..HRLLEDERSAPEIKYNS.VL
RetrocopySGGTKHPVTMATSEHVVMQNEALVALALIAALELSTAEKDLESAKLVQNSHRLLEDERSAPEIKYNSTVL
ParentalICALMGSESLHKEVQDLAFLDVVSKLRS
ICALMGSESL.KEVQDLAFL.VVSK.RS
RetrocopyICALMGSESLQKEVQDLAFLEVVSKHRS

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
SRP012049_cerebellum 0 .04 RPM 56 .36 RPM
SRP017611_brain 0 .24 RPM 106 .78 RPM
SRP017611_kidney 0 .07 RPM 12 .08 RPM
SRP017611_liver 0 .00 RPM 8 .92 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cfam_370 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_370 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_370 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG00000010267 2 retrocopies
retro_cfam_1428, retro_cfam_370 ,


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