RetrogeneDB ID:

retro_mmus_946

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:12:69920474..69921524(-)
Located in intron of:ENSMUSG00000021066
Retrocopy
information
Ensembl ID:ENSMUSG00000078370
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Gapdh
Ensembl ID:ENSMUSG00000057666
Aliases:Gapdh, Gapd
Description:glyceraldehyde-3-phosphate dehydrogenase [Source:MGI Symbol;Acc:MGI:95640]


Retrocopy-Parental alignment summary:






>retro_mmus_946
CTTGTGCGGTGCCAGCCTCGTCCCGTAGACAAAATGGTGAAGGTCGGTGTGAACGGATTTGGCCGTATTGGGCGCCTGGT
CACCAGGGCTGCCGTCTGCAGTGGCAAAATCTCCGTGGAGATTGTTGCCATCAACGACCCCTTCATTGACCTCAACTACA
TGGTCTACTTGTTCCAGTCTGACTCCACCCATGGCAAATTCAACAGAACAGTCCAGGCCGAGAATGGGAAGCTTGTCATC
AACGGGAAGCCCATCACCATCTTCCAGGAGCGAGACACACCCCCCCCCCTCGCTAACATCAAATGGGGTGATGCCGGTGC
TGACTATGTCGTGGAGTCTACTGGTGTCTTCACCACCATGGAGAAGGCCGGGGCCCACTTGAAGGGTGGAGCCAAAAGGG
TCATCATCTCCGCCCCTTCTGCCGATGCCCCCATGTTTGTGATGGGTGTGAACCACGAGAAATATGACAACTCACTCAAG
ATTGTCAGCAATGCATCCTGCACCACCAACTGCTTAGCCCCCCTGGCCAAAGTCATCCATGACAACTTTGGCATCATGGA
AGGGCTCATGACCACGGTCCATGCCATCACTGCCACCCAGAAGACTGTGGATGGCCCCTCTGGAAAGCTGTGGCGTGATG
GTCGTGGGGCTGCCCAGAACATCATCCCTGCATCCACTGGTGCTGCCAAGGCTGTGGGCAAGGTCATCCCAGAGCTGAAC
GGGAAGCTCACTGGCATGGCCTTCCGTGTTCCTACCCGAAATGTGTCTGTTGTGGATCTGACGTGCCGCCTGGAGAAACA
CGCCAAGTATGATGACATCAAGAAGGTGGTGAAGCAGGCATCTGAGGGCCCACTGAAGGGCATCTTGGGCTACACTGAGG
ACCAGGTTGTCTCCTGCGACTTCAACAACAACTCCCACTCTTCCACCTTCGATGCCGGGGCTGGCATTGCTCTCAATGAC
AACTTTGTCAAGCTCATTTCCTGGTATGACAATGAATACGGCTACAGCAACAGGATGGTGGACCTCATGGCCTACATGGC
CTCCAAGGAG

ORF - retro_mmus_946 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.43 %
Parental protein coverage: 95.82 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLRRVFPRPVDKMVKVGVNGFGRIGRLVTRAAICSGK--VEIVAINDPFIDLNYMVYMFQYDSTHGKFNGT
L.R..PRPVDKMVKVGVNGFGRIGRLVTRAA.CSGK..VEIVAINDPFIDLNYMVY.FQ.DSTHGKFN.T
RetrocopyLVRCQPRPVDKMVKVGVNGFGRIGRLVTRAAVCSGKISVEIVAINDPFIDLNYMVYLFQSDSTHGKFNRT
ParentalVKAENGKLVINGKPITIFQERDP----TNIKWGEAGAEYVVESTGVFTTMEKAGAHLKGGAKRVIISAPS
V.AENGKLVINGKPITIFQERD......NIKWG.AGA.YVVESTGVFTTMEKAGAHLKGGAKRVIISAPS
RetrocopyVQAENGKLVINGKPITIFQERDTXXXXANIKWGDAGADYVVESTGVFTTMEKAGAHLKGGAKRVIISAPS
ParentalADAPMFVMGVNHEKYDNSLKIVSNASCTTNCLAPLAKVIHDNFGIVEGLMTTVHAITATQKTVDGPSGKL
ADAPMFVMGVNHEKYDNSLKIVSNASCTTNCLAPLAKVIHDNFGI.EGLMTTVHAITATQKTVDGPSGKL
RetrocopyADAPMFVMGVNHEKYDNSLKIVSNASCTTNCLAPLAKVIHDNFGIMEGLMTTVHAITATQKTVDGPSGKL
ParentalWRDGRGAAQNIIPASTGAAKAVGKVIPELNGKLTGMAFRVPTPNVSVVDLTCRLEKPAKYDDIKKVVKQA
WRDGRGAAQNIIPASTGAAKAVGKVIPELNGKLTGMAFRVPT.NVSVVDLTCRLEK.AKYDDIKKVVKQA
RetrocopyWRDGRGAAQNIIPASTGAAKAVGKVIPELNGKLTGMAFRVPTRNVSVVDLTCRLEKHAKYDDIKKVVKQA
ParentalSEGPLKGILGYTEDQVVSCDFNSNSHSSTFDAGAGIALNDNFVKLISWYDNEYGYSNRVVDLMAYMASKE
SEGPLKGILGYTEDQVVSCDFN.NSHSSTFDAGAGIALNDNFVKLISWYDNEYGYSNR.VDLMAYMASKE
RetrocopySEGPLKGILGYTEDQVVSCDFNNNSHSSTFDAGAGIALNDNFVKLISWYDNEYGYSNRMVDLMAYMASKE

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
SRP007412_brain 0 .75 RPM 278 .65 RPM
SRP007412_cerebellum 0 .26 RPM 213 .55 RPM
SRP007412_heart 1 .71 RPM 706 .53 RPM
SRP007412_kidney 1 .06 RPM 440 .24 RPM
SRP007412_liver 0 .55 RPM 224 .28 RPM
SRP007412_testis 0 .59 RPM 22 .50 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_946 was not detected
No EST(s) were mapped for retro_mmus_946 retrocopy.
No TSS is located nearby retro_mmus_946 retrocopy 5' end.
retro_mmus_946 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_946 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 35 parental genes, and 771 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000066755 retrocopies
Ailuropoda melanoleuca ENSAMEG0000001432935 retrocopies
Bos taurus ENSBTAG000000147314 retrocopies
Canis familiaris ENSCAFG000000150774 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
Mustela putorius furoENSMPUG0000001689128 retrocopies
Mus musculus ENSMUSG00000057666 109 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,
Mus musculus ENSMUSG000000610992 retrocopies
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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