RetrogeneDB ID:

retro_cfam_15

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:32:36488433..36489546(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCAFG00000030514
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:TRAM1
Ensembl ID:ENSCAFG00000007866
Aliases:None
Description:Canis lupus familiaris translocation associated membrane protein 1 (TRAM1), mRNA. [Source:RefSeq mRNA;Acc:NM_001003267]


Retrocopy-Parental alignment summary:






>retro_cfam_15
ATGGCGTTTCGCAAGAAGAGCGCCAAGAACCCCCCGGTGCTGAGCCACGAGTTCATCCTGCAGAACCACGCGGACCTCGT
CGCCTGCGTGGGGATGTTCTTCGTGCTGGGGCTGATGTTCGAGGGCACGGCCGAGGCCTCCATCGTCTTCATCACCCTGC
AGCACAGCGTCCCCTTCCCCGCGGCCGAGGAACGAGCGCCGGAACCCAAGTTCCTCTACTACTACGGCATCAGAGACCTG
GCCACGGTGTTCTTCTACATGCTGGTGGCGATCATCATTCACGCCACCATCCAGGAGTACGTGTTGGACAAGATCAACAG
GCGGATGCAGTTCCCCAAGCCCAAGCAAAGCCGCTTTAACGAGTCGGGCCAGTTCAGCGCCTTCTACCTCGTGTCCTGTG
TCTGGGGCACGTTCATCCTGGTTTCGGAAAACTGCCTGTCGGACCCCACCCTTCTGTGGAGGGCCCCGCCTCACAACATG
ATGACCTTCCAGATGAAGTTCTTCTACATATCGCAGCTGGCTTACTGGTTCCACGCCTTCCCGGAGCTCTACTTCCAGAG
GATCAAAAAGCAGGACGTCCCGCGCCAGCTGGTCTACATCGGGCTGCACCTCTTCCACATTGCCGGAGCTTACCTGCTGT
ACCTGAACCACCTGGGCCTCGTCCTTCTGACGATGCACTACTTCGTGGAATTCCTTTCCCACATCTGTGACCTCTTCTAC
TTCAGGGACGACAAGTACCACAAGGAGTTTTCCCTGTGGGCGGTTGTGTTCGTCTCGGGCCGGTTTGTGACTCTGATCGT
CTCGGTGGTGACTGTCGGCTTTCACCTGGCAGGAGGGCAGGCTCGGAATTCCGACGCCACCGCTGGAAACGTCAACGTGC
TGGCCGCCAAAATCGCGGTGCTCTCGTCCAGTTGCACCATCCAAGCCTACATAACCTGGAATTTATTTAATGTCCAGCTG
CAGAGGTGGATGGAGGAAGACACTACCCTGCAGGCCCCAAGTGTGAAGAAGAAACGGACTAAAGGGCGGTCTTCTAGAAA
AGGAACGGAAAACGGTGTGGCGACTGCAAACAGAGTAGACTCTCCCCATAAAAGGAAAGAGAAATCTTCCTAA

ORF - retro_cfam_15 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.75 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalNHADIVSCVAMVFLLGLMFEITAKASIIFVTLQYNVTLPATEEQATESTSLYYYGIKDLATVFFYMLVAI
NHAD.V.CV.M.F.LGLMFE.TA.ASI.F.TLQ..V..PA.EE.A.E...LYYYGI.DLATVFFYMLVAI
RetrocopyNHADLVACVGMFFVLGLMFEGTAEASIVFITLQHSVPFPAAEERAPEPKFLYYYGIRDLATVFFYMLVAI
ParentalIIHAIIQEYVLDKINRRMHFSKTKHSKFNESGQLSAFYLFSCIWGTFILISENYISDPTILWRAYPHNLM
IIHA.IQEYVLDKINRRM.F.K.K.S.FNESGQ.SAFYL.SC.WGTFIL.SEN..SDPT.LWRA.PHN.M
RetrocopyIIHATIQEYVLDKINRRMQFPKPKQSRFNESGQFSAFYLVSCVWGTFILVSENCLSDPTLLWRAPPHNMM
ParentalTFQMKFFYIAQLAYWFHAFPELYFQKTKKEDIPRQLVYIGLYLFHIAGAYLLNLNHLGLVLLVLHYFVEF
TFQMKFFYI.QLAYWFHAFPELYFQ..KK.D.PRQLVYIGL.LFHIAGAYLL.LNHLGLVLL..HYFVEF
RetrocopyTFQMKFFYISQLAYWFHAFPELYFQRIKKQDVPRQLVYIGLHLFHIAGAYLLYLNHLGLVLLTMHYFVEF
ParentalLFHISRLFYFSDEKYQKGFSLWAVLFVLGRLLTLILSVLTVGFGLARAENQKLDFSAGNFNVLAVRIAVL
L.HI..LFYF.D.KY.K.FSLWAV.FV.GR..TLI.SV.TVGF.LA.......D..AGN.NVLA..IAVL
RetrocopyLSHICDLFYFRDDKYHKEFSLWAVVFVSGRFVTLIVSVVTVGFHLAGGQARNSDATAGNVNVLAAKIAVL
ParentalASICITQAFMMWKFINFQLRRW-REHSTFQAPVVKKKPTVTKGRSSRKGTENGVNGTVTSNGADSPRNRK
.S.C..QA...W...N.QL.RW..E..T.QAP.VKKK...TKGRSSRKGTENGV....T.N..DSP..RK
RetrocopySSSCTIQAYITWNLFNVQLQRWMEEDTTLQAPSVKKKR--TKGRSSRKGTENGV---ATANRVDSPHKRK
ParentalEKSS
EKSS
RetrocopyEKSS

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 19 .11 RPM 29 .15 RPM
SRP017611_brain 12 .62 RPM 29 .77 RPM
SRP017611_kidney 2 .84 RPM 122 .76 RPM
SRP017611_liver 0 .65 RPM 49 .89 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_15 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_15 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_15 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Equus caballus retro_ecab_506
Parental genes homology:
Parental genes homology involve 25 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000063251 retrocopy
retro_amel_78,
Bos taurus ENSBTAG000000075621 retrocopy
retro_btau_24,
Canis familiaris ENSCAFG00000007866 1 retrocopy
retro_cfam_15 ,
Callithrix jacchus ENSCJAG000000078931 retrocopy
retro_cjac_168,
Dasypus novemcinctus ENSDNOG000000092962 retrocopies
retro_dnov_27, retro_dnov_906,
Dipodomys ordii ENSDORG000000019011 retrocopy
retro_dord_27,
Equus caballus ENSECAG000000183781 retrocopy
retro_ecab_506,
Echinops telfairi ENSETEG000000184471 retrocopy
retro_etel_674,
Felis catus ENSFCAG000000287751 retrocopy
retro_fcat_136,
Homo sapiens ENSG000000671671 retrocopy
retro_hsap_51,
Loxodonta africana ENSLAFG000000116251 retrocopy
retro_lafr_9,
Macaca mulatta ENSMMUG000000015161 retrocopy
retro_mmul_235,
Monodelphis domestica ENSMODG000000073161 retrocopy
retro_mdom_308,
Mustela putorius furoENSMPUG000000106161 retrocopy
retro_mputfur_558,
Mus musculus ENSMUSG000000259351 retrocopy
retro_mmus_117,
Nomascus leucogenys ENSNLEG000000113761 retrocopy
retro_nleu_73,
Oryctolagus cuniculus ENSOCUG000000087341 retrocopy
retro_ocun_52,
Otolemur garnettii ENSOGAG000000063791 retrocopy
retro_ogar_2932,
Pongo abelii ENSPPYG000000186601 retrocopy
retro_pabe_169,
Pan troglodytes ENSPTRG000000203341 retrocopy
retro_ptro_2081,
Rattus norvegicus ENSRNOG000000078921 retrocopy
retro_rnor_287,
Sus scrofa ENSSSCG000000061931 retrocopy
retro_sscr_980,
Ictidomys tridecemlineatus ENSSTOG000000055371 retrocopy
retro_itri_38,
Tarsius syrichta ENSTSYG000000138871 retrocopy
retro_tsyr_24,
Tursiops truncatus ENSTTRG000000003281 retrocopy
retro_ttru_24,


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