RetrogeneDB ID:

retro_cfam_122

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:3:62264162..62265164(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCAFG00000017475
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:GAPDH
Ensembl ID:ENSCAFG00000015077
Aliases:None
Description:Canis lupus familiaris glyceraldehyde-3-phosphate dehydrogenase (GAPDH), mRNA. [Source:RefSeq mRNA;Acc:NM_001003142]


Retrocopy-Parental alignment summary:






>retro_cfam_122
ATGGTGAAGGTTGGAGTGAACGGATTTGGCCGTATTGGGCGCCTGGTCACCAGGGCTGCTTTTAACTCTGGCAAAGTGGA
TATTGTCACCATCAATGATCCCTTCATTGATCTCAACTACATGGTGTACATGTTCCAGTATGATTCTACCCACGGCAAAT
TCCACGGCACAGTCAAGGCTGAGAACGGGAAACTTGTCATCAACGGGAAGTCCATCTCCATCTTCCAGGAGCGAGATCCC
GCCAACATCAAATGGGGTGATGCTGGTGCTGAGTATGTTGTGGAGTCCACTGGGGTCTTCACCACCATGGAGAAGGCTGG
GGCTCACTTGAAAGGCAGGGCCAAGAGGGTCATCATCTCTGCTCCTTCTGCTGATGCCCCCATGTTTGTGATGGGCGTGA
ACCATGAGAAGTATGACAACTCCCTCAAGATTGTCAGCAATGCCTCCTGCACCACCAACTGCTTGGCTCCTCTAGCCAAA
GTCATCCATGACCACTTTGGCATCGTGGAGGGCCTCATGACCACCGTCCATGCCATCACTGCCACCCAGAAGACCGTGGA
CGGCCCCTCTGGGAAGCTGTGGCGTGACGGCCGAGGGGCTGCCCAGAACATCATCCCTGCTTCCACTGGCGCCGCCAAGG
CTGTGGGCAAGGTCATCCCTGAGCTGAACGGGAAGCTCACTGGCATGGCCTTCTGTGTCCCCACCCCCAATGTATCAGTT
GTGGATCTGACCTGCCGCCTGGAGAAAGCTGCCAAATATGATGACATCAAGAAGGTAGTGAAGCAGGCATCGGAGGGACC
CCTCAAGGGCATCCTGGGCTACACTGAGGACCAGGTGGTCTCCTGTGACTTCAACAGTGACACCCACTCTTCCACCTTTG
ACGCCGGGGCTGGCATTGCTCTCAATGACCACTTTGTCAAGCTCATTTCCTGGTATGACAATGAATTCGGCTACAGCAAC
TGGGTGGTGGACCTCATGGTCCACATGGCCTCCAAGGAGTAA

ORF - retro_cfam_122 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.48 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVGVNGFGRIGRLVTRAAFNSGKVDIVAINDPFIDLNYMVYMFQYDSTHGKFHGTVKAENGKLVINGKSIS
VGVNGFGRIGRLVTRAAFNSGKVDIV.INDPFIDLNYMVYMFQYDSTHGKFHGTVKAENGKLVINGKSIS
RetrocopyVGVNGFGRIGRLVTRAAFNSGKVDIVTINDPFIDLNYMVYMFQYDSTHGKFHGTVKAENGKLVINGKSIS
ParentalIFQERDPANIKWGDAGAEYVVESTGVFTTMEKAGAHLKGGAKRVIISAPSADAPMFVMGVNHEKYDNSLK
IFQERDPANIKWGDAGAEYVVESTGVFTTMEKAGAHLKG.AKRVIISAPSADAPMFVMGVNHEKYDNSLK
RetrocopyIFQERDPANIKWGDAGAEYVVESTGVFTTMEKAGAHLKGRAKRVIISAPSADAPMFVMGVNHEKYDNSLK
ParentalIVSNASCTTNCLAPLAKVIHDHFGIVEGLMTTVHAITATQKTVDGPSGKMWRDGRGAAQNIIPASTGAAK
IVSNASCTTNCLAPLAKVIHDHFGIVEGLMTTVHAITATQKTVDGPSGK.WRDGRGAAQNIIPASTGAAK
RetrocopyIVSNASCTTNCLAPLAKVIHDHFGIVEGLMTTVHAITATQKTVDGPSGKLWRDGRGAAQNIIPASTGAAK
ParentalAVGKVIPELNGKLTGMAFRVPTPNVSVVDLTCRLEKAAKYDDIKKVVKQASEGPLKGILGYTEDQVVSCD
AVGKVIPELNGKLTGMAF.VPTPNVSVVDLTCRLEKAAKYDDIKKVVKQASEGPLKGILGYTEDQVVSCD
RetrocopyAVGKVIPELNGKLTGMAFCVPTPNVSVVDLTCRLEKAAKYDDIKKVVKQASEGPLKGILGYTEDQVVSCD
ParentalFNSDTHSSTFDAGAGIALNDHFVKLISWYDNEFGYSNRVVDLMVHMASKE
FNSDTHSSTFDAGAGIALNDHFVKLISWYDNEFGYSN.VVDLMVHMASKE
RetrocopyFNSDTHSSTFDAGAGIALNDHFVKLISWYDNEFGYSNWVVDLMVHMASKE

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 2 .18 RPM 754 .89 RPM
SRP017611_brain 2 .46 RPM 1129 .59 RPM
SRP017611_kidney 0 .99 RPM 1180 .94 RPM
SRP017611_liver 0 .65 RPM 666 .33 RPM
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_122 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_122 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_122 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 34 parental genes, and 742 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000066755 retrocopies
Ailuropoda melanoleuca ENSAMEG0000001432935 retrocopies
Bos taurus ENSBTAG000000147314 retrocopies
Canis familiaris ENSCAFG000000023251 retrocopy
Canis familiaris ENSCAFG00000015077 4 retrocopies
Callithrix jacchus ENSCJAG000000082341 retrocopy
Cavia porcellus ENSCPOG000000263501 retrocopy
Equus caballus ENSECAG0000002205111 retrocopies
Erinaceus europaeus ENSEEUG000000114443 retrocopies
Echinops telfairi ENSETEG00000013749118 retrocopies
retro_etel_1011, retro_etel_1037, retro_etel_1070, retro_etel_1117, retro_etel_1132, retro_etel_1153, retro_etel_1171, retro_etel_1183, retro_etel_1214, retro_etel_1215, retro_etel_1247, retro_etel_1249, retro_etel_1255, retro_etel_1257, retro_etel_1258, retro_etel_1266, retro_etel_127, retro_etel_1320, retro_etel_1349, retro_etel_1352, retro_etel_1381, retro_etel_1386, retro_etel_1389, retro_etel_1408, retro_etel_1419, retro_etel_1422, retro_etel_1431, retro_etel_1437, retro_etel_1470, retro_etel_1473, retro_etel_1490, retro_etel_150, retro_etel_1511, retro_etel_1538, retro_etel_1550, retro_etel_1563, retro_etel_1570, retro_etel_1588, retro_etel_1601, retro_etel_1608, retro_etel_1620, retro_etel_163, retro_etel_1635, retro_etel_1641, retro_etel_1674, retro_etel_1679, retro_etel_1702, retro_etel_1738, retro_etel_1746, retro_etel_1759, retro_etel_1769, retro_etel_1776, retro_etel_1780, retro_etel_180, retro_etel_184, retro_etel_1840, retro_etel_1869, retro_etel_1895, retro_etel_1897, retro_etel_1949, retro_etel_1970, retro_etel_1976, retro_etel_1982, retro_etel_1989, retro_etel_2033, retro_etel_2076, retro_etel_209, retro_etel_212, retro_etel_213, retro_etel_2152, retro_etel_2161, retro_etel_2173, retro_etel_2198, retro_etel_2202, retro_etel_2210, retro_etel_243, retro_etel_290, retro_etel_330, retro_etel_339, retro_etel_340, retro_etel_365, retro_etel_397, retro_etel_432, retro_etel_440, retro_etel_463, retro_etel_489, retro_etel_495, retro_etel_504, retro_etel_536, retro_etel_557, retro_etel_586, retro_etel_589, retro_etel_600, retro_etel_611, retro_etel_618, retro_etel_621, retro_etel_624, retro_etel_649, retro_etel_653, retro_etel_69, retro_etel_770, retro_etel_780, retro_etel_790, retro_etel_792, retro_etel_798, retro_etel_802, retro_etel_810, retro_etel_874, retro_etel_895, retro_etel_899, retro_etel_90, retro_etel_906, retro_etel_931, retro_etel_934, retro_etel_935, retro_etel_968, retro_etel_969, retro_etel_987,
Felis catus ENSFCAG0000000687417 retrocopies
Homo sapiens ENSG0000011164042 retrocopies
Gorilla gorilla ENSGGOG0000000955330 retrocopies
Loxodonta africana ENSLAFG000000027803 retrocopies
Macropus eugenii ENSMEUG0000001527367 retrocopies
Microcebus murinus ENSMICG0000000654616 retrocopies
Myotis lucifugus ENSMLUG0000001432018 retrocopies
Macaca mulatta ENSMMUG0000001867933 retrocopies
Monodelphis domestica ENSMODG0000001806641 retrocopies
Mus musculus ENSMUSG00000057666109 retrocopies
retro_mmus_1029, retro_mmus_1082, retro_mmus_1136, retro_mmus_1193, retro_mmus_1249, retro_mmus_1319, retro_mmus_1328, retro_mmus_136, retro_mmus_1365, retro_mmus_1371, retro_mmus_1467, retro_mmus_1474, retro_mmus_1480, retro_mmus_1615, retro_mmus_1692, retro_mmus_1721, retro_mmus_1728, retro_mmus_1886, retro_mmus_1922, retro_mmus_1957, retro_mmus_1983, retro_mmus_1985, retro_mmus_2009, retro_mmus_2020, retro_mmus_2030, retro_mmus_2100, retro_mmus_211, retro_mmus_2119, retro_mmus_2122, retro_mmus_2148, retro_mmus_2158, retro_mmus_2175, retro_mmus_2206, retro_mmus_2216, retro_mmus_2248, retro_mmus_2298, retro_mmus_2370, retro_mmus_2371, retro_mmus_2389, retro_mmus_2463, retro_mmus_2477, retro_mmus_2481, retro_mmus_2512, retro_mmus_2556, retro_mmus_2587, retro_mmus_2623, retro_mmus_2626, retro_mmus_2647, retro_mmus_2681, retro_mmus_2755, retro_mmus_2761, retro_mmus_2764, retro_mmus_2848, retro_mmus_2872, retro_mmus_2911, retro_mmus_2912, retro_mmus_2913, retro_mmus_2914, retro_mmus_2915, retro_mmus_2920, retro_mmus_2932, retro_mmus_2943, retro_mmus_300, retro_mmus_3036, retro_mmus_3064, retro_mmus_3120, retro_mmus_3137, retro_mmus_3140, retro_mmus_3148, retro_mmus_3151, retro_mmus_3188, retro_mmus_3193, retro_mmus_3197, retro_mmus_3216, retro_mmus_3228, retro_mmus_3306, retro_mmus_3335, retro_mmus_3336, retro_mmus_3357, retro_mmus_3377, retro_mmus_3445, retro_mmus_3514, retro_mmus_3575, retro_mmus_3650, retro_mmus_3658, retro_mmus_3693, retro_mmus_3716, retro_mmus_3814, retro_mmus_416, retro_mmus_437, retro_mmus_48, retro_mmus_553, retro_mmus_608, retro_mmus_619, retro_mmus_628, retro_mmus_635, retro_mmus_698, retro_mmus_745, retro_mmus_765, retro_mmus_766, retro_mmus_787, retro_mmus_811, retro_mmus_893, retro_mmus_914, retro_mmus_921, retro_mmus_946, retro_mmus_952, retro_mmus_976, retro_mmus_996,
Nomascus leucogenys ENSNLEG0000000382544 retrocopies
Ornithorhynchus anatinus ENSOANG000000044921 retrocopy
Ochotona princeps ENSOPRG0000001251410 retrocopies
Procavia capensis ENSPCAG000000069289 retrocopies
Pongo abelii ENSPPYG0000000418938 retrocopies
Pan troglodytes ENSPTRG0000000457743 retrocopies
Pteropus vampyrus ENSPVAG0000001257014 retrocopies
Rattus norvegicus ENSRNOG000000186304 retrocopies
Rattus norvegicus ENSRNOG000000306382 retrocopies
Sarcophilus harrisii ENSSHAG000000149534 retrocopies
Sus scrofa ENSSSCG000000006942 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000075389 retrocopies
Tursiops truncatus ENSTTRG000000160942 retrocopies
Xenopus tropicalis ENSXETG000000339751 retrocopy



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