RetrogeneDB ID:

retro_cfam_1181

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:25:16961166..16961733(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL12
Ensembl ID:ENSCAFG00000020136
Aliases:None
Description:60S ribosomal protein L12 [Source:UniProtKB/Swiss-Prot;Acc:E2RR58]


Retrocopy-Parental alignment summary:






>retro_cfam_1181
GCTCTGAGGAGGCCAAGGTGCCAAGTCTCTTCAGTCGTCCTGAATTTGGGTTCATCTGGCACCAGCCGCCTCCACTATGC
CACCTAGGTTAGAGCCCAGTGAGATGGAACTCGCATAGCGGAGGTGCATTTGTGGGGAAGCTGGTGCCATGTCTGCCCTG
CATCCTAAGATGGGCCCCCCAGTCGGTCTCCAGAAAGGGTTAGTAATGACATCATCAAGGCAACTGGTGACTGGAAGGGT
CTGAAGATGACTGTGAAATGAACCATTCAGAAGGGACAGGCCCAGACTGAAGTGGTCCCTTCTGCTTCTGCCCTGATTAT
CAAAGTCCTCAAAGAACCACCAAGAGACAGAAAGTAGCAGAAAAGCATTAAGCACAGTGGAAATGTCACTTTTGAAGAGA
CTGTCAACAGTGCTGACAGATGTGGCACCATTCTTTAGCCAGAGAGCACTCTGGAACCATTAAGGAGATCCTTGGCGCCT
GATCCATCTGTGGCCTGCAATGTTGACGGCCACCACCCTCACCACATCATAGCTGATGTCAATGGTGGAGCAGTGTGATG
CCAAGCT

ORF - retro_cfam_1181 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.8 %
Parental protein coverage: 99.47 %
Number of stop codons detected: 5
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalARRRQRCNC-LRSSRIRVHPTPAASAMPPKFDPNEIKVVYLRCTGGEVGATSALAPKIGPL-GLSPKKVG
A.RR.RC...L.SS.I.VH..PAAS.MPP...P.E......RC..GE.GA.SAL.PK.GP....SP..V.
RetrocopyALRRPRCQV>LQSS*IWVHLAPAASTMPPRLEPSEMELA*RRCICGEAGAMSALHPKMGPP<SRSPERVS
ParentalDDIAKATGDWKGLRITVKLTIQNRQAQIEVVPSASALIIKALKEPPRDRKKQKNIKHSGNITFDEIVNIA
.DI.KATGDWKGL..TVK.TIQ..QAQ.EVVPSASALIIK.LKEPPRDRK.QK.IKHSGN.TF.E.VN.A
RetrocopyNDIIKATGDWKGLKMTVK*TIQKGQAQTEVVPSASALIIKVLKEPPRDRK*QKSIKHSGNVTFEETVNSA
ParentalR-QMRHRSLARELSGTIKEILGT-AQSVGCNVDGRHPHDIIDDINSGAVECPA
..QM.H.SLARE.SGTIKEILG....SV.CNVDG.HPH.II.D.N.GAV.C.A
RetrocopyD<QMWHHSLAREHSGTIKEILGA>DPSVACNVDGHHPHHIIADVNGGAV*CQA

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 1 .05 RPM 305 .54 RPM
SRP017611_brain 1 .11 RPM 91 .54 RPM
SRP017611_kidney 0 .66 RPM 791 .32 RPM
SRP017611_liver 0 .29 RPM 227 .18 RPM
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1181 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1181 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1181 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 16 parental genes, and 319 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001671215 retrocopies
Canis familiaris ENSCAFG00000020136 31 retrocopies
Cavia porcellus ENSCPOG0000001376918 retrocopies
Equus caballus ENSECAG0000001062217 retrocopies
Echinops telfairi ENSETEG000000069417 retrocopies
Felis catus ENSFCAG0000001030231 retrocopies
Latimeria chalumnae ENSLACG000000153733 retrocopies
Macropus eugenii ENSMEUG0000000738012 retrocopies
Myotis lucifugus ENSMLUG000000095512 retrocopies
Myotis lucifugus ENSMLUG000000134041 retrocopy
Monodelphis domestica ENSMODG000000045719 retrocopies
Mustela putorius furoENSMPUG0000001383234 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,
Rattus norvegicus ENSRNOG000000162204 retrocopies
Sarcophilus harrisii ENSSHAG000000178648 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000274257 retrocopies



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