RetrogeneDB ID: | retro_rnor_2898 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | X:20596989..20599424(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Mcm2 | ||
| Ensembl ID: | ENSRNOG00000016316 | ||
| Aliases: | None | ||
| Description: | DNA replication licensing factor MCM2 [Source:RefSeq peptide;Acc:NP_001101343] |
Retrocopy-Parental alignment summary:
>retro_rnor_2898
GCAGAGGGATTGGCCCTGGATGCTGAAGATGTGGAGGAGCTGAGAGCCAGTCAGAGTGAGGCAGCTGAGCGGGTTATGAG
GCAGCAGGACTATGAGGCTGGCAGAGGCCTGGGTTGCATGCGTCGTGGGCTGCTGTACGACAGCGACGAGGAAGATGAGG
AGCGGCCTGCCCATAAGCACCGCCACGTAGAGCGTGCCACAGAAGATGACGAGGAGGATGAAGAGATGATTGAGAGTACT
GAGAACATGGAGGACCTCAAGGGTCACTCGGTGCGCGAGTAGGTGAGCATGGCAGGGCCCAGGCTGGAGATCCACCACCG
TTTCAAGAACTTCTTGCACACCCACGTGGACAGCCATGGCCACAATGTCTTCAAGGAGTGTATCAGTGATGTGTGCAAAG
AGAACTGGGAGAGTTTGGTAGTAAATTATGAAGACCTGGCAGCCCGGGAACATATGTTGGCATGCTTCTTACCCGAGGCA
CCGGCTGAGCTGCTGCAGATCTTTGATGAGGCCGCCCTGGAAGTTGTGTTGTCCATGTATCCTAAATATGACCTCATCAC
CAACCACATTCACGTGCGCATCTCCCACCTGCCTCTGGTGGAGGAGCTGCATTCACTGAGGCAGCTACACCTGAACCAGC
TGATCCATACCAGCGGTGTGGTGACCAGTTGCACTGGAGTCCTGCCCCAGCTCAGCATGGTCAAGTATAACTGTAGCAAG
TGCAACTTTATACTGGGGCCTTTCTGCCAGTCTCAGAACCAGGAGGTGAACCTGGCTCCTGCCCTGAGTGCCAGTCAACT
GGGCCCTTTGAGATCAACATGGAGGAGACCATCTATCAGAACTACCAATGGATCCGCATCCAGGAGAGTCCCGGCAAGGT
GGTGGCTGGCCGGCTGCCCCGTTCCAAGGATGCCATCCTCCTTGCTGATCTGGTGGACAGCTGCAAGCCAGGAGACGAGA
TAGAGCTGACCAGCATTTACCACAATAATTATGATGGCTAGCTTAACACCACCAACGGCTTTCCCATCTTCGTCACCATC
ATCCTGGCCAACCATGTTGCCAAGAAGGACAACAAAGTGGCCATGGGTGAGCTCACTGATGAGGACGTGAAGATGATCAC
CAGTCTTTCCATGGATCAGCAAATCGGAGAGAAGATCTTTGCCAGCATTGCAACCTCCATCTATGGGCATGAAGACATGA
AGAGAGGCCTGGCTCTGGCCCTGTTTGGAGGGGAGCCCAAGAACCCAGGTGGAAAGCACAAGGTTCGAGGTGACATCAAT
GTGCTCTTGTGTGGGGACCCTGGCACAGTAAAGTCCCAGTTCCTCAAATAAAAAAAATTGTCCAGCCATGCCATCTTCAC
CACTGGCCAAGGTGCATCAGCTGTGGAACTCATGGCGTATGTTCAGCGGCATCCTGTCAGCAGAGAGTGGACCTTAGAGG
CTGGAGCCCTGGTTCTGGCCGACCAGGGGGTGTGTCTCATTGGTGAGTTTGACAAGATGAATGACCAGGACAGGACCAGC
ATCCACAAGGCCATGGAACAGCAAAGCATCTCCATCTTCAAGGCTGGCATCATTACCTCGCTGCAAGCCTGCTGCACCAT
CATAGCTGCTGCCAACCCCATAGGGGGCTGCCACGACCCTTCACTGATCTTCTCAGGGAATGTAGACCTCACAGAGTCCA
TCATTTCCCGCTTTGATATCCTGTGTGTGGTGAGGGACACTGTTGATCCTGTTCAGGATGATATGCTGGCCCGCTTTGTG
GTTGGCAGCCACATCAGACACCACCCCAGCAACAAGAAGGATGAAGGGGTGACCAACGGTGGTACCACAGAGCCAGCCAT
GCCCAACACATACGGTGTGGAGCCCCTGCGTGAGGAGGTCCTGAAGAAGTATATTATCTATGCCAAGGAACGGGTCTGCC
CAAAGCTCAACCAGATGGACCAGGACAAAGTGGCCAGGATGTACAGCGGCCTGAAGAAGGAGTCCATGGCAACGGGCAGT
ATTCCCATCACAGTGCGACACATCAAGTCCATGATCTGCATGGCAGAGGCCCATGCATGCATGCACCTGCGAGACTACGT
AATGGAAGATGATGTCAACATGGCCATCTGCATGATGCTGGAGAGCTTCATTGACACCCAAAAGTTCAGTGTCATGCGCA
GCATGCACAAGACTTTTGCCTGGTATCTCTCCTTCCATCGAGATAACAATGATCTGATGCTCTTCATACTGAAGCAGTTG
GTGGCTGAGCAGGTGACATACCAACATAACTGCTTTGGGGCCCAGCAGGACACCATCGAAATGCCTGAGAAGGACCTGAT
GGACAAGGCCAGGCAGATCAATATCCACAACCTCTCTGCCTTCTACGACAGCAACCTCTTCAAAATCAACAAATTCAGCC
GTGACCTGAAACGCAAGCTGATCCTACAGCAGTTC
ORF - retro_rnor_2898 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.29 % |
| Parental protein coverage: | 89.83 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | AEGLALDDEDVEELTASQREAAERAMRQRDREAGRGLGRMRRGLLYDSDEEDEERPARKRRHIERATEDG |
| AEGLALD.EDVEEL.ASQ.EAAER.MRQ.D.EAGRGLG.MRRGLLYDSDEEDEERPA.K.RH.ERATED. | |
| Retrocopy | AEGLALDAEDVEELRASQSEAAERVMRQQDYEAGRGLGCMRRGLLYDSDEEDEERPAHKHRHVERATEDD |
| Parental | EEDEEMIESIENLEDLKGHSVREWVSMAGPRLEIHHRFKNFLRTHVDSHGHNVFKERISDMCKENRESLV |
| EEDEEMIES.EN.EDLKGHSVRE.VSMAGPRLEIHHRFKNFL.THVDSHGHNVFKE.ISD.CKEN.ESLV | |
| Retrocopy | EEDEEMIESTENMEDLKGHSVRE*VSMAGPRLEIHHRFKNFLHTHVDSHGHNVFKECISDVCKENWESLV |
| Parental | VNYEDLAAREHVLAYFLPEAPAELLQIFDEAALEVVLAMYPKYDRITNHIHVRISHLPLVEELRSLRQLH |
| VNYEDLAAREH.LA.FLPEAPAELLQIFDEAALEVVL.MYPKYD.ITNHIHVRISHLPLVEEL.SLRQLH | |
| Retrocopy | VNYEDLAAREHMLACFLPEAPAELLQIFDEAALEVVLSMYPKYDLITNHIHVRISHLPLVEELHSLRQLH |
| Parental | LNQLIRTSGVVTSCTGVLPQLSMVKYNCSKCNFILGPFCQSQNQEV-KPGSCPECQSTGPFEINMEETIY |
| LNQLI.TSGVVTSCTGVLPQLSMVKYNCSKCNFILGPFCQSQNQEV..PGSCPECQSTGPFEINMEETIY | |
| Retrocopy | LNQLIHTSGVVTSCTGVLPQLSMVKYNCSKCNFILGPFCQSQNQEV<EPGSCPECQSTGPFEINMEETIY |
| Parental | QNYQRIRIQESPGKVAAGRLPRSKDAILLADLVDSCKPGDEIELTGIYHNNYDGSLNTTNGFPVFATIIL |
| QNYQ.IRIQESPGKV.AGRLPRSKDAILLADLVDSCKPGDEIELT.IYHNNYDG.LNTTNGFP.F.TIIL | |
| Retrocopy | QNYQWIRIQESPGKVVAGRLPRSKDAILLADLVDSCKPGDEIELTSIYHNNYDG*LNTTNGFPIFVTIIL |
| Parental | ANHVAKKDNKVAVGELTDEDVKMITSLSKDQQIGEKIFASIAPSIYGHEDIKRGLALALFGGEPKNPGGK |
| ANHVAKKDNKVA.GELTDEDVKMITSLS.DQQIGEKIFASIA.SIYGHED.KRGLALALFGGEPKNPGGK | |
| Retrocopy | ANHVAKKDNKVAMGELTDEDVKMITSLSMDQQIGEKIFASIATSIYGHEDMKRGLALALFGGEPKNPGGK |
| Parental | HKVRGDINVLLCGDPGTAKSQFLKYIEKVSSRAIFTTGQGASAVGLTAYVQRHPVSREWTLEAGALVLAD |
| HKVRGDINVLLCGDPGT.KSQFLK.....SS.AIFTTGQGASAV.L.AYVQRHPVSREWTLEAGALVLAD | |
| Retrocopy | HKVRGDINVLLCGDPGTVKSQFLKXXX-LSSHAIFTTGQGASAVELMAYVQRHPVSREWTLEAGALVLAD |
| Parental | RGVCLIDEFDKMNDQDRTSIHEAMEQQSISISKAGIVTSLQARCTVIAAANPIGGRYDPSLTFSENVDLT |
| .GVCLI.EFDKMNDQDRTSIH.AMEQQSISI.KAGI.TSLQA.CT.IAAANPIGG..DPSL.FS.NVDLT | |
| Retrocopy | QGVCLIGEFDKMNDQDRTSIHKAMEQQSISIFKAGIITSLQACCTIIAAANPIGGCHDPSLIFSGNVDLT |
| Parental | EPIISRFDVLCVVRDTVDPVQDEMLARFVVGSHVRHHPSNKKDEGLTNGGTTEPAMPNTYGVEPLPQEVL |
| E.IISRFD.LCVVRDTVDPVQD.MLARFVVGSH.RHHPSNKKDEG.TNGGTTEPAMPNTYGVEPL..EVL | |
| Retrocopy | ESIISRFDILCVVRDTVDPVQDDMLARFVVGSHIRHHPSNKKDEGVTNGGTTEPAMPNTYGVEPLREEVL |
| Parental | KKYIIYAKERVRPKLNQMDQDKVARMYSDLRKESMATGSIPITVRHIESMIRMAEAHARMHLRDYVMEDD |
| KKYIIYAKERV.PKLNQMDQDKVARMYS.L.KESMATGSIPITVRHI.SMI.MAEAHA.MHLRDYVMEDD | |
| Retrocopy | KKYIIYAKERVCPKLNQMDQDKVARMYSGLKKESMATGSIPITVRHIKSMICMAEAHACMHLRDYVMEDD |
| Parental | VNMAIRVMLESFIDTQKFSVMRSMRKTFARYLSFRRDNNDLLLFILKQLVAEQVTYQRNRFGAQQDTIEI |
| VNMAI..MLESFIDTQKFSVMRSM.KTFA.YLSF.RDNNDL.LFILKQLVAEQVTYQ.N.FGAQQDTIE. | |
| Retrocopy | VNMAICMMLESFIDTQKFSVMRSMHKTFAWYLSFHRDNNDLMLFILKQLVAEQVTYQHNCFGAQQDTIEM |
| Parental | PEKDLMDKARQINIHNLSAFYDSDLFKINKFSRDLKRKLILQQF |
| PEKDLMDKARQINIHNLSAFYDS.LFKINKFSRDLKRKLILQQF | |
| Retrocopy | PEKDLMDKARQINIHNLSAFYDSNLFKINKFSRDLKRKLILQQF |
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 |
|---|---|---|
| SRP017611_brain | 0 .00 RPM | 3 .81 RPM |
| SRP017611_kidney | 0 .00 RPM | 15 .77 RPM |
| SRP017611_liver | 0 .00 RPM | 4 .64 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2898 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2898 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2898 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Rattus norvegicus | ENSRNOG00000016316 | 1 retrocopy |
retro_rnor_2898 ,
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