RetrogeneDB ID:

retro_mdom_309

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:1:79717623..79718068(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000004571
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_309
TTAAGGTGCTTTGGTGGTGAAGATGGTGCCACAGCTGCTTTGGCCCTCAAAACTGGTCCTTGGATTTGTTTCCCCAAAAG
GTTGGTGATGACATTGCCAAAGTGGCTAGTGACTGGAAAGGGTGAAGGATCACAGTGAAACTTACCACTCAGAGACAGAC
TTGGATTGAGGCTGTGCCTTATGCATCAACCTTGATCATCAAACCCTAAAGGAACTTTCTCAGGACAGAAAGAAGTAGAA
AACTAACAAACATAGTGGAGATATCAGTCTCGATGAGAGCATCAACATTGCTTGACAGATGAGGCACTGATGCCTCATAA
GAGACCTCTCTGGAACCATTAAAGAGATACTTGGAACTGTCCAATCTGTGGGCTGCAATATTGATGGCAGACACTCTCAT
GGTGTCATTGGAGACATCAATAATGATGCTATGGGATGCCCAGCC

ORF - retro_mdom_309 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.71 %
Parental protein coverage: 90.91 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalLRCTGGEVGATSALAPKIGP-LGLSPKKVGDDIAKATGDWKGLRITVKLTIQNRQAQIEVVPSASALIIK
LRC.GGE.GAT.ALA.K.GP.L.L.P.KVGDDIAK...DWKG.RITVKLT.Q.RQ..IE.VP.AS.LIIK
RetrocopyLRCFGGEDGATAALALKTGP<LDLFPQKVGDDIAKVASDWKG*RITVKLTTQ-RQTWIEAVPYASTLIIK
Parental-ALKEPPRDRKKQKNIKHNGNISLDEIINIARQMRHRSLARDLSGTIKEILGTAQSVGCNIDGRHPHDVI
..LKE...DRKK.K..KH.G.ISLDE.INIA.QMRH..L.RDLSGTIKEILGT.QSVGCNIDGRH.H.VI
Retrocopy<TLKELSQDRKK*KTNKHSGDISLDESINIA*QMRH*CLIRDLSGTIKEILGTVQSVGCNIDGRHSHGVI
ParentalDDINSGAVECPA
.DIN..A..CPA
RetrocopyGDINNDAMGCPA

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 499 .55 RPM
SRP007412_cerebellum 0 .00 RPM 537 .67 RPM
SRP007412_heart 0 .00 RPM 950 .51 RPM
SRP007412_kidney 0 .00 RPM 2993 .16 RPM
SRP007412_liver 0 .00 RPM 2286 .85 RPM
SRP007412_testis 0 .00 RPM 487 .16 RPM
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_309 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_309 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 35 parental genes, and 665 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001671215 retrocopies
Bos taurus ENSBTAG000000069633 retrocopies
Canis familiaris ENSCAFG0000002013631 retrocopies
Choloepus hoffmanni ENSCHOG0000000673232 retrocopies
Callithrix jacchus ENSCJAG000000180821 retrocopy
Cavia porcellus ENSCPOG0000001376918 retrocopies
Dasypus novemcinctus ENSDNOG0000000841248 retrocopies
Equus caballus ENSECAG0000001062217 retrocopies
Echinops telfairi ENSETEG000000069417 retrocopies
Felis catus ENSFCAG0000001030231 retrocopies
Homo sapiens ENSG0000019795841 retrocopies
Gorilla gorilla ENSGGOG0000000064834 retrocopies
Latimeria chalumnae ENSLACG000000153733 retrocopies
Loxodonta africana ENSLAFG0000001766910 retrocopies
Macropus eugenii ENSMEUG0000000738012 retrocopies
Myotis lucifugus ENSMLUG000000095512 retrocopies
Myotis lucifugus ENSMLUG000000134041 retrocopy
Macaca mulatta ENSMMUG000000004222 retrocopies
Monodelphis domestica ENSMODG00000004571 9 retrocopies
Mustela putorius furoENSMPUG0000001383234 retrocopies
Mus musculus ENSMUSG000000389001 retrocopy
Oryctolagus cuniculus ENSOCUG000000049029 retrocopies
Otolemur garnettii ENSOGAG00000000597120 retrocopies
retro_ogar_1002, retro_ogar_1010, retro_ogar_1049, retro_ogar_1069, retro_ogar_1106, retro_ogar_1117, retro_ogar_1137, retro_ogar_1140, retro_ogar_1181, retro_ogar_1188, retro_ogar_1189, retro_ogar_1192, retro_ogar_1230, retro_ogar_1247, retro_ogar_1263, retro_ogar_1295, retro_ogar_1331, retro_ogar_1341, retro_ogar_1408, retro_ogar_1409, retro_ogar_1427, retro_ogar_1457, retro_ogar_1464, retro_ogar_1489, retro_ogar_1503, retro_ogar_1534, retro_ogar_1536, retro_ogar_1550, retro_ogar_1569, retro_ogar_1570, retro_ogar_1579, retro_ogar_1606, retro_ogar_1621, retro_ogar_1709, retro_ogar_1717, retro_ogar_1739, retro_ogar_1789, retro_ogar_1803, retro_ogar_1810, retro_ogar_1825, retro_ogar_1836, retro_ogar_1881, retro_ogar_1885, retro_ogar_1916, retro_ogar_1923, retro_ogar_1937, retro_ogar_1941, retro_ogar_1948, retro_ogar_1969, retro_ogar_1975, retro_ogar_1987, retro_ogar_2055, retro_ogar_2115, retro_ogar_2134, retro_ogar_2172, retro_ogar_2179, retro_ogar_2180, retro_ogar_2208, retro_ogar_2209, retro_ogar_2230, retro_ogar_2291, retro_ogar_2323, retro_ogar_2387, retro_ogar_2483, retro_ogar_2495, retro_ogar_2511, retro_ogar_2570, retro_ogar_2620, retro_ogar_2622, retro_ogar_2624, retro_ogar_2749, retro_ogar_2768, retro_ogar_2809, retro_ogar_2904, retro_ogar_2935, retro_ogar_2945, retro_ogar_2953, retro_ogar_2980, retro_ogar_3004, retro_ogar_3017, retro_ogar_303, retro_ogar_3035, retro_ogar_3128, retro_ogar_3135, retro_ogar_3164, retro_ogar_3394, retro_ogar_3489, retro_ogar_395, retro_ogar_398, retro_ogar_412, retro_ogar_427, retro_ogar_452, retro_ogar_480, retro_ogar_512, retro_ogar_513, retro_ogar_538, retro_ogar_560, retro_ogar_587, retro_ogar_624, retro_ogar_636, retro_ogar_653, retro_ogar_655, retro_ogar_667, retro_ogar_668, retro_ogar_669, retro_ogar_683, retro_ogar_700, retro_ogar_734, retro_ogar_737, retro_ogar_744, retro_ogar_747, retro_ogar_775, retro_ogar_818, retro_ogar_853, retro_ogar_868, retro_ogar_901, retro_ogar_927, retro_ogar_956, retro_ogar_962, retro_ogar_964,
Ochotona princeps ENSOPRG0000001107821 retrocopies
Procavia capensis ENSPCAG000000074693 retrocopies
Pongo abelii ENSPPYG0000001962244 retrocopies
Pan troglodytes ENSPTRG000000228081 retrocopy
Pteropus vampyrus ENSPVAG0000000092515 retrocopies
Rattus norvegicus ENSRNOG000000162204 retrocopies
Sarcophilus harrisii ENSSHAG000000178648 retrocopies
Sus scrofa ENSSSCG0000000561214 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000274257 retrocopies
Tupaia belangeri ENSTBEG0000000630425 retrocopies
Tursiops truncatus ENSTTRG0000001570015 retrocopies
Vicugna pacos ENSVPAG0000000512327 retrocopies



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