RetrogeneDB ID:

retro_cfam_224

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:26:16767635..16768586(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCAFG00000010494
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:RPLP0
Ensembl ID:ENSCAFG00000010227
Aliases:None
Description:Canis lupus familiaris ribosomal protein, large, P0 (RPLP0), mRNA. [Source:RefSeq mRNA;Acc:NM_001252137]


Retrocopy-Parental alignment summary:






>retro_cfam_224
ATGCCCAGGGAAGACAGGGCGACCTGGAAATCCAACTACTTCCTTAAGATCATCCAACTTTTGGATGATTATCCAAAATG
CTTCATTGTGGGAGCAGACAATGTGGGTTCAAAGCAGATGCAGCAGATCCGCATGTCCCTCTGCAGGAATGCTGTTGTGC
TGATGGGCAAGAACACCATGATGCGCAAGGCCATCCGAGGGCATCTGGAGAACAACCCAGCCCTGGAGAAACTGTTGCCT
CATATCCGGGGGAATGTGGGCTTTGTATTCACCAAGGAGGACCTCAGTGAGATCAGGGACATGCTGCTGGCCAATAAGGT
GCCTGCTGCTGCCCGTGCTGGTGCCATAGCTCCATGTGAAGTCACTGTGCCAGCCCTGAACACAGGTCTGGGGCCTGAGA
AGACCTTTTTCTTCCAGGCTTTAGGCATTACCACTAAGATCTTTAGGGGCACCATTGAAATCCTGAGCTATGTGCAACTG
ATTAAGACCAGAGACAAAGCGGGAGCCAGCCAAGCCACACTGCTGAACATACTGAACATCTCCCCCTTCTCCTCTGGGCT
GATCATCCAGCAGGTGTTTGATAATGGCAGCATCTACAACACTGAAGTGCTTGACATCACAGAAGAAACTCTGCATTCTC
GCTTCCTGGAGGGTGTCCGCAACATTGCCAGCGTATGTCTGCAGATAGGTTACCCTACTGTTGCATCAGTGCCCCATTCT
ATCATCAATGGATACAAGTGGGTCCTGGCTTTGTCTGTGGAAACTGATTACACCTTCCCACTTGCTGAAAAGGTCAAGGC
CTTCTTGGCTGATCCATCTGCATTTGTGGCTGCTGCTCCTGTGGCTGCTGCCACCACTGCTGCACCTGCTGCTGCCGCAG
ACCCAGCCAAGGTTGAAGCAAAGGAAGAGTTGGAATCGGACAAGGATATGGGATTTGGTCTCTTTAACTAA

ORF - retro_cfam_224 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.38 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMPREDRATWKSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQIRMSLRGKAVVLMGKNTMMRKAIRGHLE
MPREDRATWKSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQIRMSL...AVVLMGKNTMMRKAIRGHLE
RetrocopyMPREDRATWKSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQIRMSLCRNAVVLMGKNTMMRKAIRGHLE
ParentalNNPALEKLLPHIRGNVGFVFTKEDLTEIRDMLLANKVPAAARAGAIAPCEVTVPAQNTGLGPEKTSFFQA
NNPALEKLLPHIRGNVGFVFTKEDL.EIRDMLLANKVPAAARAGAIAPCEVTVPA.NTGLGPEKT.FFQA
RetrocopyNNPALEKLLPHIRGNVGFVFTKEDLSEIRDMLLANKVPAAARAGAIAPCEVTVPALNTGLGPEKTFFFQA
ParentalLGITTKISRGTIEILSDVQLIKTGDKVGASEATLLNMLNISPFSFGLIIQQVFDNGSIYNPEVLDITEET
LGITTKI.RGTIEILS.VQLIKT.DK.GAS.ATLLN.LNISPFS.GLIIQQVFDNGSIYN.EVLDITEET
RetrocopyLGITTKIFRGTIEILSYVQLIKTRDKAGASQATLLNILNISPFSSGLIIQQVFDNGSIYNTEVLDITEET
ParentalLHSRFLEGVRNVASVCLQIGYPTVASVPHSIINGYKRVLALSVETDYTFPLAEKVKAFLADPSAFVAAAP
LHSRFLEGVRN.ASVCLQIGYPTVASVPHSIINGYK.VLALSVETDYTFPLAEKVKAFLADPSAFVAAAP
RetrocopyLHSRFLEGVRNIASVCLQIGYPTVASVPHSIINGYKWVLALSVETDYTFPLAEKVKAFLADPSAFVAAAP
ParentalVAAATTAAPAAAAAPAKVEAKEESEESDEDMGFGLFD
VAAATTAAPAAAA.PAKVEAKEE..ESD.DMGFGLF.
RetrocopyVAAATTAAPAAAADPAKVEAKEEL-ESDKDMGFGLFN

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 .42 RPM 182 .53 RPM
SRP017611_brain 0 .24 RPM 65 .42 RPM
SRP017611_kidney 4 .36 RPM 860 .99 RPM
SRP017611_liver 0 .73 RPM 131 .90 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_224 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_224 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_224 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 26 parental genes, and 111 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000037562 retrocopies
retro_acar_111, retro_acar_115,
Ailuropoda melanoleuca ENSAMEG000000051444 retrocopies
retro_amel_1179, retro_amel_1194, retro_amel_1377, retro_amel_847,
Canis familiaris ENSCAFG00000010227 5 retrocopies
retro_cfam_1580, retro_cfam_224 , retro_cfam_487, retro_cfam_534, retro_cfam_693,
Choloepus hoffmanni ENSCHOG000000027452 retrocopies
retro_chof_1115, retro_chof_2341,
Callithrix jacchus ENSCJAG000000086773 retrocopies
retro_cjac_1693, retro_cjac_2840, retro_cjac_786,
Felis catus ENSFCAG000000133541 retrocopy
retro_fcat_441,
Homo sapiens ENSG000000891577 retrocopies
retro_hsap_1403, retro_hsap_1553, retro_hsap_1889, retro_hsap_2095, retro_hsap_2334, retro_hsap_512, retro_hsap_784,
Gorilla gorilla ENSGGOG000000265825 retrocopies
retro_ggor_1088, retro_ggor_1771, retro_ggor_472, retro_ggor_649, retro_ggor_650,
Macropus eugenii ENSMEUG0000001640912 retrocopies
retro_meug_1211, retro_meug_1245, retro_meug_1339, retro_meug_1410, retro_meug_1672, retro_meug_1689, retro_meug_1789, retro_meug_1800, retro_meug_1943, retro_meug_2166, retro_meug_294, retro_meug_772,
Myotis lucifugus ENSMLUG0000000197011 retrocopies
retro_mluc_1016, retro_mluc_1460, retro_mluc_1503, retro_mluc_1806, retro_mluc_1966, retro_mluc_2293, retro_mluc_268, retro_mluc_497, retro_mluc_564, retro_mluc_565, retro_mluc_882,
Macaca mulatta ENSMMUG000000091572 retrocopies
retro_mmul_2245, retro_mmul_939,
Mustela putorius furoENSMPUG000000030554 retrocopies
retro_mputfur_1632, retro_mputfur_362, retro_mputfur_426, retro_mputfur_910,
Mus musculus ENSMUSG000000672742 retrocopies
retro_mmus_143, retro_mmus_2249,
Nomascus leucogenys ENSNLEG0000000029211 retrocopies
retro_nleu_1080, retro_nleu_1365, retro_nleu_1419, retro_nleu_1470, retro_nleu_1551, retro_nleu_1639, retro_nleu_1686, retro_nleu_1722, retro_nleu_2058, retro_nleu_2927, retro_nleu_3095,
Oryctolagus cuniculus ENSOCUG000000057492 retrocopies
retro_ocun_293, retro_ocun_376,
Otolemur garnettii ENSOGAG000000038434 retrocopies
retro_ogar_2184, retro_ogar_2294, retro_ogar_556, retro_ogar_713,
Procavia capensis ENSPCAG000000164296 retrocopies
retro_pcap_232, retro_pcap_314, retro_pcap_339, retro_pcap_353, retro_pcap_408, retro_pcap_67,
Petromyzon marinus ENSPMAG000000013391 retrocopy
retro_pmar_6,
Pongo abelii ENSPPYG000000050225 retrocopies
retro_pabe_2113, retro_pabe_3035, retro_pabe_568, retro_pabe_66, retro_pabe_749,
Pteropus vampyrus ENSPVAG000000031103 retrocopies
retro_pvam_114, retro_pvam_62, retro_pvam_745,
Rattus norvegicus ENSRNOG000000011483 retrocopies
retro_rnor_1350, retro_rnor_2092, retro_rnor_2970,
Sarcophilus harrisii ENSSHAG000000016232 retrocopies
retro_shar_286, retro_shar_413,
Ictidomys tridecemlineatus ENSSTOG000000113274 retrocopies
retro_itri_1155, retro_itri_276, retro_itri_331, retro_itri_982,
Tarsius syrichta ENSTSYG000000097327 retrocopies
retro_tsyr_1133, retro_tsyr_130, retro_tsyr_1376, retro_tsyr_1429, retro_tsyr_727, retro_tsyr_75, retro_tsyr_84,
Tursiops truncatus ENSTTRG000000056581 retrocopy
retro_ttru_965,
Vicugna pacos ENSVPAG000000121562 retrocopies
retro_vpac_234, retro_vpac_45,


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