RetrogeneDB ID:

retro_cfam_1937

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:8:8492945..8493800(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RSL1D1
Ensembl ID:ENSCAFG00000018865
Aliases:None
Description:ribosomal L1 domain containing 1 [Source:HGNC Symbol;Acc:24534]


Retrocopy-Parental alignment summary:






>retro_cfam_1937
ATGGAGGGTTGAGCTTCCACCACACTGTCATCCTCAGCCGCAGCCTCAGCCTCTGCCCCAGCTACCCTGGCCTGCCTGGG
GCAGCTGGACAAAGGGCAGATTAGAAAAGTGGTGGAAGCTCTGTTGGCACACTCCAGGTCCAGGAAGAACGCAAATGGAT
TGCTTTTGAATGAGAATGAAAATCTCTTTTTAATGGTAGTATTATGGAAGATTCCAAGTAAAGAACTGAGGGTCAGACTG
CCCTTGCTTCATGGTATTCGATCAGATTTAACAGATACTTGTTTACTTCCTCAGGATGAACCCAATTTAACTCCTGAAAA
GACAGAACGGTTTTACAAGAAGCTTTTGAACAAGCATGGAATTAAAACTGTTTCTTAGATTATCCCCCTCCGAACTCTAA
AAAAGGCATATAAAGCTTATGAAGCCAAGCTGTGCCTCTTGGGCAGTTTTGACTTCTTCCTTACTGATGCGAGAATCAGG
TGGCTCTTACCGTCACACCTCGGGAGACATTTCTACCACGGAAAGAACATGCTGGTACCTCTGAACCTTCTGGCCAAGAA
TGTATCCAGGGAGATTAATGAATGCATAGGTAGCACTGTCTTAAACATCTCTAAAAGTGGTTCTTGCAATACTATCCACG
CTGGCCACACTGGAATGGAGGTTGAACACATCATTGATAACATCATCTCTGTGACAAAGAGGCTTTCACAAAAGTTGCCA
GAGAAGTGGGAGAGCATGAAACTCTTTTATGTGAAGACGGAGACGTAGGCCTCCTTGCCCGTCTTTTCCTCACTTGTCAG
CTGTCAGGATGAAGCCAAGGGAATATGCACTCCTAGTCAGAAGAAAAAGGAAGCA

ORF - retro_cfam_1937 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.21 %
Parental protein coverage: 58.16 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMEGSAPPSPSSSTAASASAPETPACLEQLDKGQIRKAVEALLAHSRSRKNANGLLLNENENFFLMVILWK
MEG.A....SSS.AASASAP.T.ACL.QLDKGQIRK.VEALLAHSRSRKNANGLLLNENEN.FLMV.LWK
RetrocopyMEG*ASTTLSSSAAASASAPATLACLGQLDKGQIRKVVEALLAHSRSRKNANGLLLNENENLFLMVVLWK
ParentalIPSKELRVRLALPHGIRSDLTDICLLTKDEPNLTPENTERFYKKLLNKHGIKTISQIIPLRTLKKEYKAY
IPSKELRVRL.L.HGIRSDLTD.CLL..DEPNLTPE.TERFYKKLLNKHGIKT.S.IIPLRTLKK.YKAY
RetrocopyIPSKELRVRLPLLHGIRSDLTDTCLLPQDEPNLTPEKTERFYKKLLNKHGIKTVS*IIPLRTLKKAYKAY
ParentalEAKLRLLGSFDFFLTDARIRRLLPSHLGRHFYHRKKVPVPVNLLAKNLSREINECIGGTVLNISKSGSCS
EAKL.LLGSFDFFLTDARIR.LLPSHLGRHFYH.K...VP.NLLAKN.SREINECIG.TVLNISKSGSC.
RetrocopyEAKLCLLGSFDFFLTDARIRWLLPSHLGRHFYHGKNMLVPLNLLAKNVSREINECIGSTVLNISKSGSCN
ParentalTIRVGHTGMEVEHIVDNIIAVAKRLSQKLPEKWESVKLLYVKTERSASLPIFSSFVSCQDEAKGICTRIQ
TI..GHTGMEVEHI.DNII.V.KRLSQKLPEKWES.KL.YVKTE..ASLP.FSS.VSCQDEAKGICT..Q
RetrocopyTIHAGHTGMEVEHIIDNIISVTKRLSQKLPEKWESMKLFYVKTET*ASLPVFSSLVSCQDEAKGICTPSQ
ParentalRKKEA
.KKEA
RetrocopyKKKEA

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 .00 RPM 36 .54 RPM
SRP017611_brain 0 .00 RPM 28 .90 RPM
SRP017611_kidney 0 .00 RPM 18 .23 RPM
SRP017611_liver 0 .00 RPM 29 .30 RPM
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1937 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1937 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1937 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG00000018865 2 retrocopies
retro_cfam_1937 , retro_cfam_691,
Choloepus hoffmanni ENSCHOG000000108272 retrocopies
Callithrix jacchus ENSCJAG000000083751 retrocopy
Cavia porcellus ENSCPOG000000106303 retrocopies
Loxodonta africana ENSLAFG000000136641 retrocopy
Myotis lucifugus ENSMLUG000000007841 retrocopy
Monodelphis domestica ENSMODG000000294942 retrocopies
Otolemur garnettii ENSOGAG000000151511 retrocopy
Rattus norvegicus ENSRNOG000000486081 retrocopy
Sarcophilus harrisii ENSSHAG000000167051 retrocopy



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