RetrogeneDB ID:

retro_mdom_552

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:1:279865067..279866036(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GAPDH
Ensembl ID:ENSMODG00000018066
Aliases:None
Description:Glyceraldehyde-3-phosphate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:F7G487]


Retrocopy-Parental alignment summary:






>retro_mdom_552
TTTGTCCATATTGGACACCTGTTCACCAGGGCAGTATTCAATTCCAAAGGAGTTGATGTTGTGGCCATCAATGACTCCTT
CATTGGCCTCAAATACACAGATTACACTTTCCAATATGATTCCACTCATGGCAAGTTCAAGGGCACTGTAAAGGCAGAGA
ATGGAAAGCTGGTGATCAATGGAAAAGCCATTACCATCTTCCAGGAGTGGGTTCCCTCCAACATTAAATGAGGAGATGCT
GGAACCAAGTTCATTATGGAGTCCACTGGTGTCTTTACCACCATCTAAAATGTCAAGGCTCACTTGAAGGGTGGAGCCAA
GTGAGTCATTATCTCTGCCCCTTCTGTTGATGCCCCAATTTTGAGATGGGGTGAACCAGGAGAAATATAATTCCCTCAAA
ATGGTCAGTAATGCCTTCTGCACTACCTACTGCTTTGTCCTCTTGGCCAAGGTCATTCATGACAACTTTAGCATTGTGGA
AGGACTCATGATCACAGTCATGCCATTATCACTACCCAAAAGACAGTAGATGGACCCTTTGGCAAGCTATGGTGTGATGG
GCATGGTGCTGCACAGAGTATCATCCCTACTTCCATTGGTGCTGCCAAGGCTATGGGCAAGTTCATACTTGAGCTGAATA
GGAAGCTCACAGGCATGACCTTTCATATTCCTACTGCCAATGTTTCTATGGTAGATCTGACTTGCCACCTGGAGAAAGCT
GCCAAATTTGATGACATTAAGAAGATATTGAAGCAAGCTGCAGAGGGATACTTGAAGGGCATCTTGGGCTACACAGAGGA
CCAGGTTGTATCCTGTGACTTGAACAGTGATACCTACTCTTCTAACTTCAATGCTGGTGCTGGCATTGCCCTCAATAACC
ATTTTGTCAAGTTCATTTCTAGGAATGACAATGAGTACGGTTATAGTCACCATATAGTAGATCACATGCTGTACATGGCC
TTCAAGGAG

ORF - retro_mdom_552 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.7 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalFGRIGRLVTRAAFHSDKVEVVAINDPFIDLDYMVYMFQYDSTHGKFKGTVKAENGKLVINGKAITISQER
F..IG.L.TRA.F.S..V.VVAIND.FI.L.Y..Y.FQYDSTHGKFKGTVKAENGKLVINGKAITI.QE.
RetrocopyFVHIGHLFTRAVFNSKGVDVVAINDSFIGLKYTDYTFQYDSTHGKFKGTVKAENGKLVINGKAITIFQEW
ParentalDPANIKWGDAGAEYVVESTGVFTTMEKAGAHLKGGAKRVIISAPSADA-PMFVMG-VNHEKYDNSLKIVS
.P.NIK.GDAG.....ESTGVFTT.....AHLKGGAK.VIISAPS.DA.P.F.MG.VN.EKY.NSLK.VS
RetrocopyVPSNIK*GDAGTKFIMESTGVFTTI*NVKAHLKGGAK*VIISAPSVDA<PNFEMG<VNQEKY-NSLKMVS
ParentalNASCTTNCLAPLAKVIHDNFGIVEGLMTTV-HAITATQKTVDGPSGKLWRDGRGAAQNIIPASTGAAKAV
NA.CTT.C...LAKVIHDNF.IVEGLM.TV.HAI..TQKTVDGP.GKLW.DG.GAAQ.IIP.S.GAAKA.
RetrocopyNAFCTTYCFVLLAKVIHDNFSIVEGLMITV<HAIITTQKTVDGPFGKLWCDGHGAAQSIIPTSIGAAKAM
ParentalGKVIPELNGKLTGMAFRVPTPNVSVVDLTCRLEKAAKYDDIKKVVKQASEGALKGILGYTEDQVVSCDFN
GK.I.ELN.KLTGM.F..PT.NVS.VDLTC.LEKAAK.DDIKK..KQA.EG.LKGILGYTEDQVVSCD.N
RetrocopyGKFILELNRKLTGMTFHIPTANVSMVDLTCHLEKAAKFDDIKKILKQAAEGYLKGILGYTEDQVVSCDLN
ParentalSDTHSSTFDAGAGIALNDHFVKLISWYDNEYGYSHRVVDLMAYMATKE
SDT.SS.F.AGAGIALN.HFVK.IS..DNEYGYSH..VD.M.YMA.KE
RetrocopySDTYSSNFNAGAGIALNNHFVKFISRNDNEYGYSHHIVDHMLYMAFKE

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 .00 RPM 0 .00 RPM
SRP007412_cerebellum 0 .33 RPM 0 .00 RPM
SRP007412_heart 0 .20 RPM 0 .00 RPM
SRP007412_kidney 1 .32 RPM 0 .00 RPM
SRP007412_liver 0 .50 RPM 0 .00 RPM
SRP007412_testis 0 .00 RPM 0 .00 RPM
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_552 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_552 was not experimentally validated.

Retrocopy orthology:
Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:
Parental genes homology involve 34 parental genes, and 769 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 ENSMODG00000018066 41 retrocopies
Mustela putorius furoENSMPUG0000001689128 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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