RetrogeneDB ID:

retro_cfam_2072

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:X:44319634..44321194(+)
Located in intron of:ENSCAFG00000028692
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GSPT1
Ensembl ID:ENSCAFG00000018856
Aliases:None
Description:G1 to S phase transition 1 [Source:HGNC Symbol;Acc:4621]


Retrocopy-Parental alignment summary:






>retro_cfam_2072
GCACCTGTGGAACATTCCAAAGAGGAACAGTTAGTGTTGCGTGAAGGTTCCAATTCAGCCGTTACCATGGAACTTTCAGA
ACCTGTTGTAGAAAATGGAGAGGTGGAGATGATCCTAGAAGAGTCATGGGAGCACGATAAAGAAGTAAGTGAAGCTGAAC
CAGGGGGTAGTTCCTTGGGAGATTCGGGTCCCCCAGAAGAAAGTGGCCAGGAAATGATGGAGAAAGAGGAAGTGAGAAAA
TCTAAATCTGTGATGGTGCCCTCAGGTGCTCCTAAAAAAGAACACGTAAATGTGGTATTCATTGGGCACGTAGATGCTGG
AAAGTCAACCATTGGAGGACAAATAATGTTTTTGACAGGAATGGTTGACAAAAGGACACTTGAGAAATATGAGAGAGAAG
CTAAAGAAAAAAACAGAGAAACTTGGTATTTGTCCTGGGCCTTAGATACAAACCAGGAAGAACGAGACAAGGGTAAAACA
GTAGAAGTGGGTCGTGCCTATTTTGAAACAGAAAAGAAACATTTCACCATTTTAGATGCTCCTGGCCACAAGAGTTTTGT
CCCAAATATGATCGGTGGTGCTTCTCAAGCTGATCTGGCTGTACTGGTGATTTCTGCCAGGAAAGGAGAATTTGAAACTG
GATTTGAGAAAGGTGGACAGACAAGAGAACATGCGATGTTGGCAAAAACAGCAGGTGTAAAACATTTAGTAGTGCTTATT
AATAAGATGGATGACCCCACAGTTAATTGGAGCAGCGAGAGATATGAAGAATGTAAAGAAAAACTGGTGCCCTTTTTGAA
AAAAGTTGGCTTTAGTCCCAAAAAGGACATCCACTTTATGCCCTGCTCAGGGCTTACTGGGGCAAATATTAAAGAGCAAT
CTGATTTTTGCCCATGGTACACTGGATTACCATTTATTCCGTATTTGGATAATATGCCAAACTTCAACAGATCAATTGAT
GGACCAATTAGGCTGCCAATTGTGGATAAGTACAAGGATATGGGCACTGTGGTCCTGGGAAAGCTGGAATCAGGATCCAT
TTTTAAGGGCCAGCAGCTTGTGATGATGCCGAACAAGCACAATGTGGAAGTTCTTGGAATTCTTTCTGATGATGCTGAAA
CTGATTATGTAGCCCCAGGAGAAAACCTTAAAATCAGACTGAAGGGAATTGAAGAAGAGGAGATTCTTCCAGGATTCATA
CTGTGTGACCCTAATAATCTGTGCCATTCTGGACGCACATTTGATGTTCAGATAGTGATTATTGAACACAAGTCCATCAT
TTGTCCGGGCTATAATGCGGTGCTGCACATTCATACTTGTATTGAGGAAGTTGAGATAACGGCCTTAATCTCCTTAGTAG
ACAAAAAGTCAGGAGAGAAAAGTAAGACACGGCCCCGCTTTGTGAAACAAGATCAAGTGTGCATTGCCCGTTTAAGGACA
GCAGGAACTATCTGCCTTGAAACGTTCAAAGATTTTCCTCAGATGGGTCGTTTTACTTTAAGAGATGAGGGTAAGACCAT
TGCCATTGGAAAAGTTCTGAAACTGGTCCCAGAGAAAGAC

ORF - retro_cfam_2072 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.32 %
Parental protein coverage: 99.81 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalAPVEPSQEEQSLLCEGSNSAVSMELSEPVVENGETEMSPEESWEHKEEISEAELGGCSMGDGRAAEESAQ
APVE.S.EEQ..L.EGSNSAV.MELSEPVVENGE.EM..EESWEH..E.SEAE.GG.S.GD....EES.Q
RetrocopyAPVEHSKEEQLVLREGSNSAVTMELSEPVVENGEVEMILEESWEHDKEVSEAEPGGSSLGDSGPPEESGQ
ParentalEMMEEEEEIPKPKSVVAPPGAPKKEHVNVVFIGHVDAGKSTIGGQIMYLTGMVDKRTLEKYEREAKEKNR
EMME.EE...K.KSV..P.GAPKKEHVNVVFIGHVDAGKSTIGGQIM.LTGMVDKRTLEKYEREAKEKNR
RetrocopyEMMEKEE-VRKSKSVMVPSGAPKKEHVNVVFIGHVDAGKSTIGGQIMFLTGMVDKRTLEKYEREAKEKNR
ParentalETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVISARKG
ETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVISARKG
RetrocopyETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVISARKG
ParentalEFETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWSNERYEECKEKLVPFLKKVGFNPKKDIHF
EFETGFEKGGQTREHAMLAKTAGVKHL.VLINKMDDPTVNWS.ERYEECKEKLVPFLKKVGF.PKKDIHF
RetrocopyEFETGFEKGGQTREHAMLAKTAGVKHLVVLINKMDDPTVNWSSERYEECKEKLVPFLKKVGFSPKKDIHF
ParentalMPCSGLTGANLKEQSDFCPWYTGLPFIPYLDNLPNFNRSVDGPIRLPIVDKYKDMGTVVLGKLESGSICK
MPCSGLTGAN.KEQSDFCPWYTGLPFIPYLDN.PNFNRS.DGPIRLPIVDKYKDMGTVVLGKLESGSI.K
RetrocopyMPCSGLTGANIKEQSDFCPWYTGLPFIPYLDNMPNFNRSIDGPIRLPIVDKYKDMGTVVLGKLESGSIFK
ParentalGQQLVMMPNKHNVEVLGILSDDVETDSVAPGENLKIRLKGIEEEEILPGFILCDPNNLCHSGRTFDAQIV
GQQLVMMPNKHNVEVLGILSDD.ETD.VAPGENLKIRLKGIEEEEILPGFILCDPNNLCHSGRTFD.QIV
RetrocopyGQQLVMMPNKHNVEVLGILSDDAETDYVAPGENLKIRLKGIEEEEILPGFILCDPNNLCHSGRTFDVQIV
ParentalIIEHKSIICPGYNAVLHIHTCIEEVEITALICLVDKKSGEKSKTRPRFVKQDQVCIARLRTAGTICLETF
IIEHKSIICPGYNAVLHIHTCIEEVEITALI.LVDKKSGEKSKTRPRFVKQDQVCIARLRTAGTICLETF
RetrocopyIIEHKSIICPGYNAVLHIHTCIEEVEITALISLVDKKSGEKSKTRPRFVKQDQVCIARLRTAGTICLETF
ParentalKDFPQMGRFTLRDEGKTIAIGKVLKLVPEKD
KDFPQMGRFTLRDEGKTIAIGKVLKLVPEKD
RetrocopyKDFPQMGRFTLRDEGKTIAIGKVLKLVPEKD

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 13 .36 RPM 56 .15 RPM
SRP017611_brain 13 .18 RPM 40 .89 RPM
SRP017611_kidney 3 .10 RPM 50 .25 RPM
SRP017611_liver 0 .58 RPM 49 .31 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

1 EST(s) were mapped to retro_cfam_2072 retrocopy
EST ID Start End Identity Match Mis-match Score
DN400109 44319580 44320133 98.8 548 4 543

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_2072 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_2072 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 25 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000095891 retrocopy
retro_amel_4,
Bos taurus ENSBTAG000000035772 retrocopies
retro_btau_1793, retro_btau_1840,
Canis familiaris ENSCAFG00000018856 1 retrocopy
retro_cfam_2072 ,
Callithrix jacchus ENSCJAG000000181911 retrocopy
retro_cjac_618,
Cavia porcellus ENSCPOG000000093811 retrocopy
retro_cpor_73,
Equus caballus ENSECAG000000211951 retrocopy
retro_ecab_739,
Echinops telfairi ENSETEG000000182491 retrocopy
retro_etel_1626,
Felis catus ENSFCAG000000222811 retrocopy
retro_fcat_1913,
Gorilla gorilla ENSGGOG000000040711 retrocopy
retro_ggor_2906,
Microcebus murinus ENSMICG000000141371 retrocopy
retro_mmur_28,
Myotis lucifugus ENSMLUG000000007921 retrocopy
retro_mluc_98,
Macaca mulatta ENSMMUG000000231781 retrocopy
retro_mmul_118,
Monodelphis domestica ENSMODG000000047281 retrocopy
retro_mdom_1420,
Mustela putorius furoENSMPUG000000145041 retrocopy
retro_mputfur_147,
Mus musculus ENSMUSG000000622031 retrocopy
retro_mmus_238,
Nomascus leucogenys ENSNLEG000000101991 retrocopy
retro_nleu_2705,
Oryctolagus cuniculus ENSOCUG000000047591 retrocopy
retro_ocun_1664,
Otolemur garnettii ENSOGAG000000070831 retrocopy
retro_ogar_100,
Pteropus vampyrus ENSPVAG000000050091 retrocopy
retro_pvam_1426,
Rattus norvegicus ENSRNOG000000023351 retrocopy
retro_rnor_2931,
Sarcophilus harrisii ENSSHAG000000059081 retrocopy
retro_shar_14,
Ictidomys tridecemlineatus ENSSTOG000000154061 retrocopy
retro_itri_109,
Tupaia belangeri ENSTBEG000000088732 retrocopies
retro_tbel_3810, retro_tbel_4659,
Tarsius syrichta ENSTSYG000000138122 retrocopies
retro_tsyr_1169, retro_tsyr_148,
Tursiops truncatus ENSTTRG000000116301 retrocopy
retro_ttru_12,


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