RetrogeneDB ID:

retro_cfam_2038

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:JH373600.1:21385..24063(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCAFG00000004851
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cfam_2038
ATGGCGGCTCACCTAAAGAAACCAGTGTGCGAGGAATTCACTAAGGTGGTCCAGCAACAACAGGAGGAAATTGCAACCAA
GAAACTGCGATTGACAAAACCAAGTAAATCTGCAGCACTCCACGTAGATCGCTGTAAAGCTCCCTCCCCAGCGGATGCTT
TTCAGTATCTACTCCAGTTTGCCAGAAAGCCTTTTGAAGCAGAAAGTGAGGAAGGAGTAGTCAGGATTCTCTTGGAACAT
TGTTACAAGGAGAGTGATCCATCTGTGAGACTGAAAATTGCCTCATTGTTGGGTTTATTATCAAAGACTGCAGGGTTTTC
ACCAGACTGCATTATGGATGATGCCATTAACATCCTGCAGAATGAAAAGTTTCATCACGTCCTTGCTCAACTGTTGGACA
CCTTGCTTGCAATTGGCACCAAACTCCCAGAGAATCAAGCTATCCACATGGGATTAGTTGATGTAGCCTGCAAGCACCTC
ACAGATACATCTCCTGGTGTAAGAAATAAGTGCCTGCAATTACTTGGCAATCTTGGCTCTTTGGAGACAAGTGTCACAAA
AGATGGAGAAGGCCTAGCTCTCAGAGATGTCCAGAAGATTATAGGGGATTACTTCAGTGACCAAGACCCATGTGTCAGAA
GAGCGGCTATAAAAGCCATGTTGCAGCTTCATGAAAGAGGACTGAAATTACACCAAGCAATTTATAATCAGGCCTCTAAA
TTGTTGTCGGATGACTGTGAACAAGTGCGCAGTGCTGCAGTCCAACTTACCTGGGCTATCAGTCAGCTCTATCCTGAAAG
CACTGTCCCCATTCCTTCTTCTAATGAAGAAATTCGCTTAGTTGATGATGCATTTGGAGCAATTTGTCCCATGGTCAGTG
ATGGCTCCTGGGTGGTTCGAGTTCAGGCTGCAAAGCTATTGGGCTCGATGGAACAAGTCAGTTTTCACTTCTTGGAGCAG
ACGCTCGACAAGAAGCTCATGTCAGATCTCAGGAGAAAACGCACTACACATGATTGTACCGAGGAACTTTACAGGTCAGG
AGAGTTAACCAGTGGCTGAATGTGGGGAGGTGATGCTCCCAAAGAAGAAATAGATACAGGAGCTGTGAACTTGATGGAGT
CAGGAGCTTGTGGAGCCTTTGTTCCTGGATTGGAAGATGAGATGTATGAGGTCCGCATTGCTACTTTGGAGGCTCTCTGC
ATGCTGGCCCAATCTTCACCTTCTTTTGCGGAGAAGTGCCGCCCTGATTTCCTGGTGGACATGTTTAATGATGAAATTGA
GGAAGTACGTCTGCAGTCCATACACAGCATGAGAAAAATTTCTAATAATATCACCCTCCGAGAGGATCAGCTTGGCAGTG
TCCTGGCTGTGTTAGAGGATCGTCCAGAGATATTCGAGAGGCTGGCTCTTCACGAACTTTTATGCTGTACTAATGTTTCG
ACTAAAGAAGGGATTCATCTCGCACTGGCGGAGCTGCTGAAAAATTTAACCAAGTACTCTACTGATAGGGACTCTATATG
GAAGTGCTTGAAGTTTCTGGGAAGTCGGCATCCAACCCTGGTGCTTCCCTTGGTGCCAGAGCGCCTGAGCACCCATCCAT
TTTTTGACCCAGCTGAACCAGACATGGATGACCCAGCTTACATTGCAGTTTTGGTTCTTATTTTTAATGCTGCTACAACC
TGTCCAACAATGCCAGCACTATTCTCAGATCATACCTTCAGGCATTATGCCTACCTCCGAGACAGTCTTTCTCATCTTGT
TCCTGCCTTAAGGTTATCAGGTAGAGAACTAGTGTCATCGGCCGTTTCTCCCGGTATTGCGCCCCATGAAGACCCGTCCC
ATCAGTTCCTGCAGCAGAGCCCTGAAAGGGTGTACAGTCTCCAGAGCACCGGGACCCTCAGGGAACCCAGAAGCTGCTGG
AGTTCACCATCCGGGATCTGCAAAGACTTAGAGAACTTCAGTCTGAACTAGCAGGAGTTGCTGACTTCTCGGCTACCTAT
CTTTGGTGTCAGCTTCTTCTCATCAAGGCCTTGCAAGGAAAGCTGTGGAATGTGGCTGCCCCTTTATATTTGAAGCAGAG
TGACTTGGCCTCCGCAGCAGCAAAACAGATCATGGAAGAGACCTACAAAATGGAGTTCATGTACAGTGGTGTGGAGGAGA
AACAGGTGGTGATTATACATCCCATGAGGCTGCAGGCCAAAGCCTTGCAACTTACAGTAACAGCACGGACTACTCGAGGA
GTTGACCCCTTATTTGGGATGTGTGAAAACTTTTTACAGGAAGTGGACTTTTTTCAGAGGTGTTTTATTGCTGATTTGCC
CCCACCTACAGGACAGCTTTGTGGACAAACTTCTTGACCTTATGCCCCGACTCATGACATCCAAGCCTGTGGAAGTGGTC
AAAATTATACAGACCATGCTGAGGCAGAGTACCTCCTTGCACCTCCCCCTTCCAGAGCAGATCCACATACTTCAGCCACC
ATCATTGAGCCAGCAGGCGAGTCAGGCAACCCTTTGCGGTTTACGTCTGGATTGGTTGTGGCCCTGGATGTCGATGCGAC
CCTGGAACATGTGCAGGACCCTGAGAGTGCTGTGAAGGTCCAGGTCTTCTATCCAGATGGCCAGGCTCAGATGATTCATC
CTAAGCCGGCAGACTTGAGGAATCCTGGCCCACCCAGG

ORF - retro_cfam_2038 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.84 %
Parental protein coverage: 92.32 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMAAHLKKRVYEEFTKVVQQQQEEIATKKLRLTKPSKSAALHIDLCKATSPADALQYLLQFARKPVEAESV
MAAHLKK.V.EEFTKVVQQQQEEIATKKLRLTKPSKSAALH.D.CKA.SPADA.QYLLQFARKP.EAES.
RetrocopyMAAHLKKPVCEEFTKVVQQQQEEIATKKLRLTKPSKSAALHVDRCKAPSPADAFQYLLQFARKPFEAESE
ParentalEGVVRILLEHYYKENDPSVRLKIASLLGLLSKTAGFSPDCIMDDAINILQNEKSHQVLAQLLDTLLAIGT
EGVVRILLEH.YKE.DPSVRLKIASLLGLLSKTAGFSPDCIMDDAINILQNEK.H.VLAQLLDTLLAIGT
RetrocopyEGVVRILLEHCYKESDPSVRLKIASLLGLLSKTAGFSPDCIMDDAINILQNEKFHHVLAQLLDTLLAIGT
ParentalKLPENQAIQIRLVDVACKHLTDTSHGVRNKCLQLLGNLGSLEKSVTKDGEGLAVRDVQKIIGDYFSDQDP
KLPENQAI...LVDVACKHLTDTS.GVRNKCLQLLGNLGSLE.SVTKDGEGLA.RDVQKIIGDYFSDQDP
RetrocopyKLPENQAIHMGLVDVACKHLTDTSPGVRNKCLQLLGNLGSLETSVTKDGEGLALRDVQKIIGDYFSDQDP
ParentalRVRTAAIKAMLQLHERGLKLHQAIYNQACKLLSDDYEQVRSAAVQLIWVVSQLYPESIVPIPSSNEEIRL
.VR.AAIKAMLQLHERGLKLHQAIYNQA.KLLSDD.EQVRSAAVQL.W..SQLYPES.VPIPSSNEEIRL
RetrocopyCVRRAAIKAMLQLHERGLKLHQAIYNQASKLLSDDCEQVRSAAVQLTWAISQLYPESTVPIPSSNEEIRL
ParentalVDDAFGKICHMVSDGSWVVRVQAAKLLGSMEQVSSHFLEQTLDKKLMSDLRRKRTAHERAKELYSSGEFS
VDDAFG.IC.MVSDGSWVVRVQAAKLLGSMEQVS.HFLEQTLDKKLMSDLRRKRT.H....ELY.SGE..
RetrocopyVDDAFGAICPMVSDGSWVVRVQAAKLLGSMEQVSFHFLEQTLDKKLMSDLRRKRTTHDCTEELYRSGELT
ParentalSGRKWGDDAPKEEIDTGAVNLIESGACGAFVHGLEDEMYEVRIAAVEALCMLAQSSPSFAEKCL-DFLVD
SG..WG.DAPKEEIDTGAVNL.ESGACGAFV.GLEDEMYEVRIA..EALCMLAQSSPSFAEKC..DFLVD
RetrocopySG*MWGGDAPKEEIDTGAVNLMESGACGAFVPGLEDEMYEVRIATLEALCMLAQSSPSFAEKCRPDFLVD
ParentalMFNDEIEEVRLQSIHTMRKISNNITLREDQLDTVLAVLEDSSRDI-REALHELLCCTNVSTKEGIHLALV
MFNDEIEEVRLQSIH.MRKISNNITLREDQL..VLAVLED......R.ALHELLCCTNVSTKEGIHLAL.
RetrocopyMFNDEIEEVRLQSIHSMRKISNNITLREDQLGSVLAVLEDRPEIFERLALHELLCCTNVSTKEGIHLALA
ParentalELLKNLTKYPTDRDSIWKCLKFLGSRHPTLVLPLVPELLSTHPFFDTAEPDMDDPAYIAVLVLIFNAAKT
ELLKNLTKY.TDRDSIWKCLKFLGSRHPTLVLPLVPE.LSTHPFFD.AEPDMDDPAYIAVLVLIFNAA.T
RetrocopyELLKNLTKYSTDRDSIWKCLKFLGSRHPTLVLPLVPERLSTHPFFDPAEPDMDDPAYIAVLVLIFNAATT
ParentalCPTMPALFSDHTFRHYAYLRDSLSHLVPALRLPGRKLVSSAVSPSIAPHEDPSHQFLQQSLERVYSLQHL
CPTMPALFSDHTFRHYAYLRDSLSHLVPALRL.GR.LVSSAVSP.IAPHEDPSHQFLQQS.ERVYSLQ..
RetrocopyCPTMPALFSDHTFRHYAYLRDSLSHLVPALRLSGRELVSSAVSPGIAPHEDPSHQFLQQSPERVYSLQST
Parental-DPQG-TQELLEFTIRDLQRLGELQSELAGVADFSATYLRCQLLLIKALQEKLWNVAAPLYLKQSDLASA
..P.G.TQ.LLEFTIRDLQRL.ELQSELAGVADFSATYL.CQLLLIKALQ.KLWNVAAPLYLKQSDLASA
Retrocopy>GPSG>TQKLLEFTIRDLQRLRELQSELAGVADFSATYLWCQLLLIKALQGKLWNVAAPLYLKQSDLASA
ParentalAAKQIMEETYKMEFMYSGVENKQVVIIHHMRLQAKALQLIVTARTTRGVDPLFGMCEKFLQEVDFFQRCF
AAKQIMEETYKMEFMYSGVE.KQVVIIH.MRLQAKALQL.VTARTTRGVDPLFGMCE.FLQEVDFFQRCF
RetrocopyAAKQIMEETYKMEFMYSGVEEKQVVIIHPMRLQAKALQLTVTARTTRGVDPLFGMCENFLQEVDFFQRCF
ParentalIADL-PHLQDSFVDKLLDLMPRLMTSKPVEVVKILQTMLRQSTFLHLPLPEQIH-KASATIIEPAGESDN
IADL.PHLQDSFVDKLLDLMPRLMTSKPVEVVKI.QTMLRQST.LHLPLPEQIH...SATIIEPAGES.N
RetrocopyIADL>PHLQDSFVDKLLDLMPRLMTSKPVEVVKIIQTMLRQSTSLHLPLPEQIH<HTSATIIEPAGESGN
ParentalPLRFTSGLVVALDVDATLEHVQDPQSTVKVQVLYPDGQAQMIHPKPADFRNPGPGR
PLRFTSGLVVALDVDATLEHVQDP.S.VKVQV.YPDGQAQMIHPKPAD.RNPGP.R
RetrocopyPLRFTSGLVVALDVDATLEHVQDPESAVKVQVFYPDGQAQMIHPKPADLRNPGPPR

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 .46 RPM 22 .39 RPM
SRP017611_brain 0 .00 RPM 15 .32 RPM
SRP017611_kidney 0 .00 RPM 10 .24 RPM
SRP017611_liver 0 .07 RPM 10 .22 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_2038 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_2038 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_2038 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 ENSCAFG00000004851 2 retrocopies
retro_cfam_2021, retro_cfam_2038 ,


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