RetrogeneDB ID:

retro_cfam_1674

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:4:74624254..74625252(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:LDHB
Ensembl ID:ENSCAFG00000012195
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cfam_1674
ATGGCAACTCTTAAGGAAATACTGATTGCACCAATTGCAGAAGAAGAGGCAGCGATCCCAAACAATAAGATCACTGTAGT
AGGTGTTGGACAAGTTGGTATGGCATGTGCCACCAGCATTCTGGGAAAGTCTCTGGCTGATGAACTTGCCCTTGTGGATG
TTTTAGAAGATAAACTCAAAGGAGAAATGATGGATCTAAAGCATAGGAGCTTATTTCTTCAGACACCTAAAATTGTGGCA
GATAAAGATTACTCTGTGACTGCCAATTCTATGATTGTGGTGGTGACTGCAGGAGTCCGACAGCAGGAGGGAGAGAGCTG
CCTCAATCTAGTGCAAAGGAATGTTAATGTCTTCAAATTCATTATTCCTCAGATAGTCAAGTACAGTCCTAATTGTATCA
TAATTGTGGTTTCCAACCCAGTGGATATTCTTACATATGTTACCTGGAAACTAAGTGGACTACCCAAGCAATGTGCGATT
GGAAGTGGGTGTAATCTGGATTCTGCTAGATTTCACTATTTTATGGCTGAAAAACTTGGCATTCATCCCAGCAGCTACCA
TGGATGAATTTGGGGAGAACATGGCGATGCAAGTGTGGCTGTGTGGAGTGGAATGAATGTGGCACGTGTTTCTCTTCAAG
AACTGAATCCAGAAATAGGAACAGACAACGAGAGTGAAAATTGGAAGGAAGTGTATAAGATGGTGGTTGAAAGTGCCTAT
GAAGTCATCAAGTTAAAACGATATACCAACTGGGCTATTGGAGTAAGTGTGGCTGATCTCATTGAATCCATGTTGAAAAA
TCTCTCCAGGATTCATTCAGTGTCAACAATGGTGAAGGGCATGTATGGTATTAAGAAGAGTCTTCCTGTGTCTTCCGTGT
ATCCTGAAGCTCGGGGCGTTCCAGTGTGATCAACCGGAAGCTAAAGGATGATGAGGTTGCCCAGCTCAAGAAAAGTGCAG
ATACCTTGTGGGATATCCAGAAGGACCTAAAAGATCTG

ORF - retro_cfam_1674 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.76 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 1
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMATLKEKLIAPVAEEEAAIPNNKITVVGVGQVGMACAISILGKSLADELALVDVLEDKLKGEMMDLQHGS
MATLKE.LIAP.AEEEAAIPNNKITVVGVGQVGMACA.SILGKSLADELALVDVLEDKLKGEMMDL.H.S
RetrocopyMATLKEILIAPIAEEEAAIPNNKITVVGVGQVGMACATSILGKSLADELALVDVLEDKLKGEMMDLKHRS
ParentalLFLQTPKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCIIIVVSNP
LFLQTPKIVADKDYSVTANS.IVVVTAGVRQQEGES.LNLVQRNVNVFKFIIPQIVKYSP.CIIIVVSNP
RetrocopyLFLQTPKIVADKDYSVTANSMIVVVTAGVRQQEGESCLNLVQRNVNVFKFIIPQIVKYSPNCIIIVVSNP
ParentalVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSSVAVWSGVNVAGV
VDILTYVTWKLSGLPK...IGSGCNLDSARF.Y.MAEKLGIHPSS.HG.I.GEHGD.SVAVWSG.NVA.V
RetrocopyVDILTYVTWKLSGLPKQCAIGSGCNLDSARFHYFMAEKLGIHPSSYHG*IWGEHGDASVAVWSGMNVARV
ParentalSLQELNPEMGTDNDSENWKEVHKMVVESAYEVIKLKGYTNWAIGLSVADLIESMLKNLSRIHPVSTMVKG
SLQELNPE.GTDN.SENWKEV.KMVVESAYEVIKLK.YTNWAIG.SVADLIESMLKNLSRIH.VSTMVKG
RetrocopySLQELNPEIGTDNESENWKEVYKMVVESAYEVIKLKRYTNWAIGVSVADLIESMLKNLSRIHSVSTMVKG
ParentalMYGIENEVFLSLPCILNARGL-TSVINQKLKDDEVAQLKKSADTLWDIQKDLKDL
MYGI......S......ARG...SVIN.KLKDDEVAQLKKSADTLWDIQKDLKDL
RetrocopyMYGIKKSLPVS-SVYPEARGV<SSVINRKLKDDEVAQLKKSADTLWDIQKDLKDL

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 .00 RPM 92 .61 RPM
SRP017611_brain 0 .00 RPM 105 .67 RPM
SRP017611_kidney 0 .00 RPM 329 .39 RPM
SRP017611_liver 0 .00 RPM 7 .47 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_1674 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_1674 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1674 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 29 parental genes, and 86 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000161754 retrocopies
retro_amel_1316, retro_amel_814, retro_amel_882, retro_amel_977,
Bos taurus ENSBTAG000000196034 retrocopies
retro_btau_1589, retro_btau_303, retro_btau_451, retro_btau_647,
Canis familiaris ENSCAFG000000092118 retrocopies
retro_cfam_1061, retro_cfam_1149, retro_cfam_1182, retro_cfam_1317, retro_cfam_1617, retro_cfam_1946, retro_cfam_2006, retro_cfam_309,
Canis familiaris ENSCAFG00000012195 9 retrocopies
retro_cfam_1068, retro_cfam_111, retro_cfam_1674 , retro_cfam_17, retro_cfam_1700, retro_cfam_174, retro_cfam_1836, retro_cfam_701, retro_cfam_93,
Choloepus hoffmanni ENSCHOG000000076581 retrocopy
retro_chof_1145,
Cavia porcellus ENSCPOG000000071381 retrocopy
retro_cpor_762,
Dasypus novemcinctus ENSDNOG000000136204 retrocopies
retro_dnov_1161, retro_dnov_1511, retro_dnov_1570, retro_dnov_529,
Echinops telfairi ENSETEG000000199551 retrocopy
retro_etel_850,
Felis catus ENSFCAG000000126391 retrocopy
retro_fcat_462,
Homo sapiens ENSG000001117161 retrocopy
retro_hsap_4863,
Gorilla gorilla ENSGGOG000000157581 retrocopy
retro_ggor_3033,
Loxodonta africana ENSLAFG000000009722 retrocopies
retro_lafr_197, retro_lafr_315,
Macropus eugenii ENSMEUG000000048251 retrocopy
retro_meug_311,
Microcebus murinus ENSMICG000000171832 retrocopies
retro_mmur_275, retro_mmur_300,
Myotis lucifugus ENSMLUG000000121551 retrocopy
retro_mluc_202,
Macaca mulatta ENSMMUG000000026794 retrocopies
retro_mmul_212, retro_mmul_303, retro_mmul_308, retro_mmul_315,
Monodelphis domestica ENSMODG000000177861 retrocopy
retro_mdom_1484,
Mustela putorius furoENSMPUG000000001725 retrocopies
retro_mputfur_1300, retro_mputfur_1561, retro_mputfur_492, retro_mputfur_539, retro_mputfur_549,
Mus musculus ENSMUSG000000302464 retrocopies
retro_mmus_1817, retro_mmus_2035, retro_mmus_2509, retro_mmus_335,
Oryctolagus cuniculus ENSOCUG000000220151 retrocopy
retro_ocun_805,
Otolemur garnettii ENSOGAG000000047639 retrocopies
retro_ogar_1469, retro_ogar_2093, retro_ogar_2344, retro_ogar_2459, retro_ogar_3288, retro_ogar_3342, retro_ogar_3383, retro_ogar_689, retro_ogar_721,
Pongo abelii ENSPPYG000000043563 retrocopies
retro_pabe_1738, retro_pabe_1744, retro_pabe_3780,
Pan troglodytes ENSPTRG000000047621 retrocopy
retro_ptro_3237,
Pteropus vampyrus ENSPVAG000000024623 retrocopies
retro_pvam_1487, retro_pvam_320, retro_pvam_673,
Rattus norvegicus ENSRNOG000000130003 retrocopies
retro_rnor_2697, retro_rnor_2749, retro_rnor_2834,
Sorex araneus ENSSARG000000025651 retrocopy
retro_sara_713,
Sus scrofa ENSSSCG000000005761 retrocopy
retro_sscr_37,
Ictidomys tridecemlineatus ENSSTOG000000220582 retrocopies
retro_itri_501, retro_itri_648,
Tarsius syrichta ENSTSYG000000137597 retrocopies
retro_tsyr_1130, retro_tsyr_1532, retro_tsyr_1860, retro_tsyr_2051, retro_tsyr_334, retro_tsyr_64, retro_tsyr_986,


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