RetrogeneDB ID:

retro_cfam_2134

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:X:12287948..12289247(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCAFG00000012233
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ENO3
Ensembl ID:ENSCAFG00000015802
Aliases:None
Description:enolase 3 (beta, muscle) [Source:HGNC Symbol;Acc:3354]


Retrocopy-Parental alignment summary:






>retro_cfam_2134
ATGTCTATTCTCAAGATCCACGCCAGGGAGATCTTTGACTCTCGTGGGAACCCCACTGTTGAGGTTGACCTCTACACCTC
CAAAGGTCTCTTCAGAGCTGCTGTGCCCAGTGGTGCCTCCACTGGTATCTACGAGGCCCTCGAGCTCCGGGACAATGACA
AGACACGCTACATGGGGAAAGGTGTCTCAAAGGCTGTTGAGCACATCAATAAAACTATTGCACCTGCCCTGGTTAGCAAG
AAAGTGAACGTTGTGGAGCAGGAAAAGATTGACAAACTGATGATCAAGATGGACGGGACAGAGAATAAATCTAAATTTGG
TGCAAATGCCATTCTGGAGTGTCCCTGGCTGTCTGCAAGGCGGGGGCTGTCGAGAAGGGGGTGCCCCTGTACCGCCACAT
TGCTGATTTGGCTGGCAATTCTGAAGTTATCCTGCCAGTTCCGGCTTTCAATGTCATCAAGGTGGTTCCCATGCTGGCAA
CAAGCTGGCCATGCAGGAGTTCATGATCCTTCCCGTTGGTGCAGCGAACTTCAAGGAGGCCATGCGCATCGGAGCAGAGG
TTTATCACAACCTGAAGAATGTCATCAAGGAGAAATATGGAAAAGATGCCACCAATGTGGGCGATGAAGGTGGATTTGCT
CCTAATATCCTGGAGAACAAAGAAGCTCTGGAACTGCTGAAGAATGCCATCGGGAAGGCTGGCTACACCGATAAGGTGGT
CATCGGCATGGACATAGCTGCTTCCGAGTTCTTCAGGTCTGGAAGTATGACCTGGACTTCAAGTCCCCTGATGACCCCAG
CAGGTACATCACGCCTGACCAGCTGGCTGACCTCTACAAGTCCTTCATCAGGAACTACCCAGTGGCGTCTTTTGAAGACC
CCTTCAACCAGGATGACTGGGAAGTTTGGCAGAACTTCACTGCCAGCGCTGGAATCCAAGTGGTGGGGGACGATCTCACC
GTGACCAACCCGAAGCAGATTTCCAAGGCTGTGGGCAAGAAATCGTGCAACTGCCTCCTGCTTAAAGTGAACCAGATTGG
CTCTGTGACCGAGTCTCTTCAGGCGTGCAAGCTGGCCCAGTCCAATGGGTGGGGCGTCATGGTGTCGCATCGCTCTGGGG
AGACCAAAGATACCTTTATCGCTGACCTGGTGGTGGGACTCTGCACTGGGCAGGTCAAGACAGGTGCACCATGCAGATCC
GAGCGCTTGGCCAAGTACAACCAGATCCTCAGAATTGAAGAGGAACTGGGTAGCAAGGCCAAGTTCGTCGGCAGAAGCTT
CAGAAACCCCCTTGCCAAG

ORF - retro_cfam_2134 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.01 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMAMQKIFAREILDSRGNPTVEVDLHTAKGRFRAAVPSGASTGIYEALELRDGDKSRYLGKGVLKAVEHIN
M...KI.AREI.DSRGNPTVEVDL.T.KG.FRAAVPSGASTGIYEALELRD.DK.RY.GKGV.KAVEHIN
RetrocopyMSILKIHAREIFDSRGNPTVEVDLYTSKGLFRAAVPSGASTGIYEALELRDNDKTRYMGKGVSKAVEHIN
ParentalKTLGPALLEKKLSVVDQEKVDKFMIELDGTENKSKFGANAIL-GVSLAVCKAGAAEKGVPLYRHIADLAG
KT..PAL..KK..VV.QEK.DK.MI..DGTENKSKFGANAIL.GVSLAVCKAGA.EKGVPLYRHIADLAG
RetrocopyKTIAPALVSKKVNVVEQEKIDKLMIKMDGTENKSKFGANAIL<GVSLAVCKAGAVEKGVPLYRHIADLAG
ParentalNPDLVLPVPAFNVIN-GGSHAGNKLAMQEFMILPVGASSFREAMRIGAEVYHHLKGVIKAKYGKDATNVG
N....LPVPAFNVI..GGSHAGNKLAMQEFMILPVGA..F.EAMRIGAEVYH.LK.VIK.KYGKDATNVG
RetrocopyNSEVILPVPAFNVIK<GGSHAGNKLAMQEFMILPVGAANFKEAMRIGAEVYHNLKNVIKEKYGKDATNVG
ParentalDEGGFAPNILENNEALELLKTAIQAAGYPDKVVIGMDVAASEFYRNG-KYDLDFKSPDDPARHITGEKLG
DEGGFAPNILEN.EALELLK.AI..AGY.DKVVIGMD.AASEF.R.G.KYDLDFKSPDDP.R.IT...L.
RetrocopyDEGGFAPNILENKEALELLKNAIGKAGYTDKVVIGMDIAASEFFRSG<KYDLDFKSPDDPSRYITPDQLA
ParentalELYKSFIKNYPVVSIEDPFDQDDWATWTSFLSGVNIQIVGDDLTVTNPKRIAQAVEKKACNCLLLKVNQI
.LYKSFI.NYPV.S.EDPF.QDDW..W..F.....IQ.VGDDLTVTNPK.I..AV.KK.CNCLLLKVNQI
RetrocopyDLYKSFIRNYPVASFEDPFNQDDWEVWQNFTASAGIQVVGDDLTVTNPKQISKAVGKKSCNCLLLKVNQI
ParentalGSVTESIQACKLAQSNGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSERLAKYNQLMRIEEAL
GSVTES.QACKLAQSNGWGVMVSHRSGET.DTFIADLVVGLCTGQ.KTGAPCRSERLAKYNQ..RIEE.L
RetrocopyGSVTESLQACKLAQSNGWGVMVSHRSGETKDTFIADLVVGLCTGQVKTGAPCRSERLAKYNQILRIEEEL
ParentalGDKAVFAGRKFRNPKAK
G.KA.F.GR.FRNP.AK
RetrocopyGSKAKFVGRSFRNPLAK

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 32 .26 RPM 15 .88 RPM
SRP017611_brain 34 .14 RPM 6 .51 RPM
SRP017611_kidney 49 .20 RPM 3 .30 RPM
SRP017611_liver 18 .56 RPM 20 .38 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_2134 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_2134 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_2134 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 4 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000145231 retrocopy
retro_cfam_320,
Canis familiaris ENSCAFG00000015802 2 retrocopies
retro_cfam_1010, retro_cfam_2134 ,
Callithrix jacchus ENSCJAG000000116792 retrocopies
retro_cjac_115, retro_cjac_177,
Macropus eugenii ENSMEUG0000000791525 retrocopies
retro_meug_1019, retro_meug_1341, retro_meug_1483, retro_meug_1540, retro_meug_1566, retro_meug_1605, retro_meug_170, retro_meug_1701, retro_meug_1743, retro_meug_1869, retro_meug_1905, retro_meug_1929, retro_meug_2026, retro_meug_2190, retro_meug_235, retro_meug_269, retro_meug_578, retro_meug_607, retro_meug_637, retro_meug_803, retro_meug_820, retro_meug_906, retro_meug_965, retro_meug_973, retro_meug_976,




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