RetrogeneDB ID:

retro_cfam_195

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:11:15345518..15347129(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCAFG00000000576
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCAFG00000030409
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cfam_195
ATGGCGCTCACCAGCTTTTTACCTGCACCTACTCAGCTATCTCAGGACCAACTTGAGGCTGAAGAAAAAGCAAGATCCCA
GAGATCAAGACAGACCTCACTGGTCTCATCCCGAAGAGAACCTCCCCCATATGGGTACAGGAAAGGCTGGATACCTCGAT
TATTAGAGGATTTTGGAGATGGAGGTGCTTTTCCAGAGATCCATGTGGCCCAGTATCCACTGGATATGGGACGAAAGAAA
AAAATGTCAAATGCACTGACCATTCAGGTGGATGCTGAAGGAAAAATTAAATATGATGCAATTGCTCGGCAAGGACAGTC
AAAAGACAAGGTCATTTATAGCAAGTATACTGACCTGGTTCCCAAGGAAGTCATGAATGCAGATGATCCAGATCTGCAAA
GACCTGATGAAGAAGCCATTAAAGAGATAACAGAAAAGACAAGAGTAGCCTTAGAAAAATCTGTATCACAGAAGGTTGCT
GCAGCCATGCCAGTTCGAGCTGCTGATAAACTGGCTCCTGCTCAGTATATTCGATACACACCATCTCAGCAAGGAGTGGC
TTTCAACTCTGGAGCTAAACAGAGAGTTATTCGGATGGTAGAAATGCAGAAAGATCCAATGGAGCCTCCAAGATTCAAGA
TTAATAAGAAAATTCCCCAAGGACCACCTTCTCCTCCTGCACCTGTCATGCATTCTCCTAGCCGAAAGATGACTGTGAAG
GAGCAACAAGAATGGAAGATTCCTCCTTGTATTTCAAACTGGAAAAATGCAAAGGGGTATACAATTCCATTAGACAAACG
TCTGGCTGCTGATGGAAGAGGCCTGCAGACAGTTCACATCAATGAGAATTTTGCTAAGCTGGCCGAAGCCCTCTATATTG
CTGATCGGAAGGCTCGTGAAGCTGTAGAAATGCGTGCTCAAGTAGAGAGAAAGATGGCACAAAAAGAAAAGGAGAAACAT
GAAGAGAAACTTAGAGAAATGGCCCAGAAAGCTAGAGAGAGAAGAGCTGGGATTAAAACTCATGTGGAAAAAGAGGATGG
GGAGGCACGTGAGAGGGATGAAATCCGGCATGACAGGCGAAAAGAGAGACAACACGACCGGAATCTTTCCAGGGCAGCTC
CTGATAAGCGGTCAAAACTACAGAGAAATGAAAATCGAGATATCAGTGAAGTCATTGCTCTTGGTGTGCCCAATCCGCGG
ACGTCCAATGAAGTTCAGTATGACCAAAGCCTCTTCAACCAGTCGAAGGGTATGGACAGTGGTTTTGCAGGTGGAGAAGA
TGAAATTTACAACGTTTATGATCAAGCCTGGAGAGGTGGTAAAGATATGGCCCAGAATATTTACAGGCCCAGTAAAAATC
TGGACAAGGACATGTATGGTGATGACCTAGAAGCCAGAATAAAGACCAACAGATTTGTTCCCGATAAGGAGTTTTCTGGT
TCAGACCGTAGGCAAAGAGGCCGAGAAGGACCAGTTCAGTTTGAGGAAGATCCTTTTGGTTTGGACAAGTTTTTGGAAGA
GGCCAAACAGCACGGTGGCTCTAAAAGACCCTCAGACAGCAGCCGCCCCAAGGAACATGAGCATGAAGGCAAGAAGAGGA
GGAAGGAGTAG

ORF - retro_cfam_195 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.44 %
Parental protein coverage: 99.25 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalSFLPAPTQLSQDQLEAEEKARSQRSRQTSLVSSRREPPPYGYRKGWIPRLLEDFGDGGAFPEIHVAQYPL
SFLPAPTQLSQDQLEAEEKARSQRSRQTSLVSSRREPPPYGYRKGWIPRLLEDFGDGGAFPEIHVAQYPL
RetrocopySFLPAPTQLSQDQLEAEEKARSQRSRQTSLVSSRREPPPYGYRKGWIPRLLEDFGDGGAFPEIHVAQYPL
ParentalDMGRKKKMSNALAIQVDAEGKIKYDAIARQGQSKDKVIYSKYTDLVPKEVMNADDPDLQRPDEEAIKEIT
DMGRKKKMSNAL.IQVDAEGKIKYDAIARQGQSKDKVIYSKYTDLVPKEVMNADDPDLQRPDEEAIKEIT
RetrocopyDMGRKKKMSNALTIQVDAEGKIKYDAIARQGQSKDKVIYSKYTDLVPKEVMNADDPDLQRPDEEAIKEIT
ParentalEKTRVALEKSVSQKVAAAMPVRAADKLAPAQYIRYTPSQQGVAFNSGAKQRVIRMVEMQKDPMEPPRFKI
EKTRVALEKSVSQKVAAAMPVRAADKLAPAQYIRYTPSQQGVAFNSGAKQRVIRMVEMQKDPMEPPRFKI
RetrocopyEKTRVALEKSVSQKVAAAMPVRAADKLAPAQYIRYTPSQQGVAFNSGAKQRVIRMVEMQKDPMEPPRFKI
ParentalNKKIPRGPPSPPAPVMHSPSRKMTVKEQQEWKIPPCISNWKNAKGYTIPLDKRLAADGRGLQTVHINENF
NKKIP.GPPSPPAPVMHSPSRKMTVKEQQEWKIPPCISNWKNAKGYTIPLDKRLAADGRGLQTVHINENF
RetrocopyNKKIPQGPPSPPAPVMHSPSRKMTVKEQQEWKIPPCISNWKNAKGYTIPLDKRLAADGRGLQTVHINENF
ParentalAKLAEALYIADRKAREAVEMRAQVERKMAQKEKEKHEEKLREMAQKARERRAGIKTHVEKEDGEARERDE
AKLAEALYIADRKAREAVEMRAQVERKMAQKEKEKHEEKLREMAQKARERRAGIKTHVEKEDGEARERDE
RetrocopyAKLAEALYIADRKAREAVEMRAQVERKMAQKEKEKHEEKLREMAQKARERRAGIKTHVEKEDGEARERDE
ParentalIRHDRRKERQHDRNLSRAAPDKRSKLQRNENRDISEVIALGVPNPRTSNEVQYDQRLFNQSKGMDSGFAG
IRHDRRKERQHDRNLSRAAPDKRSKLQRNENRDISEVIALGVPNPRTSNEVQYDQ.LFNQSKGMDSGFAG
RetrocopyIRHDRRKERQHDRNLSRAAPDKRSKLQRNENRDISEVIALGVPNPRTSNEVQYDQSLFNQSKGMDSGFAG
ParentalGEDEIYNVYDQAWRGGKDMAQNIYRPSKNLDKDMYGDDLEARIKTNRFVPDKEFSGSDRRQRGREGPVQF
GEDEIYNVYDQAWRGGKDMAQNIYRPSKNLDKDMYGDDLEARIKTNRFVPDKEFSGSDRRQRGREGPVQF
RetrocopyGEDEIYNVYDQAWRGGKDMAQNIYRPSKNLDKDMYGDDLEARIKTNRFVPDKEFSGSDRRQRGREGPVQF
ParentalEEDPFGLDKFLEEAKQHGGSKRPSDSSRPKEHEHEGKKRRKE
EEDPFGLDKFLEEAKQHGGSKRPSDSSRPKEHEHEGKKRRKE
RetrocopyEEDPFGLDKFLEEAKQHGGSKRPSDSSRPKEHEHEGKKRRKE

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 2 .23 RPM 19 .32 RPM
SRP017611_brain 0 .48 RPM 11 .91 RPM
SRP017611_kidney 0 .92 RPM 18 .03 RPM
SRP017611_liver 0 .80 RPM 7 .54 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_195 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_195 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_195 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 21 parental genes, and 33 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000039762 retrocopies
retro_amel_163, retro_amel_912,
Canis familiaris ENSCAFG00000030409 1 retrocopy
retro_cfam_195 ,
Callithrix jacchus ENSCJAG000000169472 retrocopies
retro_cjac_2932, retro_cjac_576,
Dipodomys ordii ENSDORG000000123803 retrocopies
retro_dord_693, retro_dord_781, retro_dord_782,
Felis catus ENSFCAG000000016371 retrocopy
retro_fcat_635,
Homo sapiens ENSG000001006031 retrocopy
retro_hsap_174,
Gorilla gorilla ENSGGOG000000260161 retrocopy
retro_ggor_257,
Loxodonta africana ENSLAFG000000034822 retrocopies
retro_lafr_474, retro_lafr_787,
Myotis lucifugus ENSMLUG000000052282 retrocopies
retro_mluc_387, retro_mluc_805,
Monodelphis domestica ENSMODG000000052521 retrocopy
retro_mdom_1841,
Mustela putorius furoENSMPUG000000087241 retrocopy
retro_mputfur_551,
Mus musculus ENSMUSG000000210392 retrocopies
retro_mmus_1022, retro_mmus_387,
Nomascus leucogenys ENSNLEG000000167711 retrocopy
retro_nleu_982,
Otolemur garnettii ENSOGAG000000298251 retrocopy
retro_ogar_1404,
Ochotona princeps ENSOPRG000000075681 retrocopy
retro_opri_737,
Pongo abelii ENSPPYG000000060311 retrocopy
retro_pabe_454,
Pan troglodytes ENSPTRG000000065871 retrocopy
retro_ptro_165,
Sorex araneus ENSSARG000000022793 retrocopies
retro_sara_403, retro_sara_568, retro_sara_727,
Tupaia belangeri ENSTBEG000000140743 retrocopies
retro_tbel_2575, retro_tbel_2927, retro_tbel_3536,
Taeniopygia guttata ENSTGUG000000123402 retrocopies
retro_tgut_15, retro_tgut_30,
Tarsius syrichta ENSTSYG000000109511 retrocopy
retro_tsyr_1871,


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