RetrogeneDB ID: | retro_rnor_588 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 1:84689819..84692243(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSRNOG00000050758 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Epc2 | ||
| Ensembl ID: | ENSRNOG00000029447 | ||
| Aliases: | None | ||
| Description: | enhancer of polycomb homolog 2 [Source:RefSeq peptide;Acc:NP_001102051] |
Retrocopy-Parental alignment summary:
>retro_rnor_588
ATGAGTAAACTCTCCTTCCGAGCGCGGGCGCTGGACGCCGCCAAACCGCTGCCCATCTACCGCGGCAAGGACATGCCTGA
TCTCAACGACTGCGTCTCCATCAACCGGGCCGTGCCCCAGATGCCCACCGGGATGGAGAAGGAGGAGGAATCGGAACATC
ACTTACAGCGAGCTATTTCAGCACAGCAAGTATTTAGAGAAAAAAACGAGAGCATGGTCATTCCAGTTCCTGAGGCGGAG
AGCAACGTCAACTATTACAATCGCTTGTACAAAGGGGAGTTTAAACAGCCCAAACAGTTCATTCATATTCAGCCTTTTAA
CCTAGACAATGAGCAACCAGATTATGATATGGATTCTGAAGATGAGACATTATTAAATAGACTTAACAGAAAGATGGAAG
TTAAACCTTTGCAATTTGAAATTATGATTGACAGACTTGAAAAAGCCAGTTCTAACCAGCTTGTAACACTTCAAGAAGCA
GAACTGCTGCTGAATGAAGACGACTACCTTATTAAAGCTGTATATGACTACTGGGTGAGGAAAAGCAAGAACTGCAGGGG
GCCGTCCCTCATCCCCCAGATTAAGCAAGAGAAGAGAGATGGCTCTACCAACAATGATCCGTATGTTGCCTTTCGGAGGA
GAACAGAGAAGATGCAGACTCGGAAGAACCGTAAGAATGATGAGGCTTCTTATGAAAAGATGCTGAAGCTGAGGCGGGAG
TTCAGCAGAGCCATAACAATTTTGGAAATGATTAAGAGAAGAGAGAAAACCAAACGGGAATTATTGCACTTAACGCTGGA
AGTTGTGGAAAAAAGATATCATTTGGGAGACTATGGGGGTGAAATCCTTAATGAAGTGAAAGTTAATAGATCAGAAAAAG
AGTTATATGCCAGTCCAGCAACTCTTCATAATGGAAATCATCACAAAGTTCAAGAATGTAAAACTAAGCACCCTCATCAT
TTGTCTTTGAAAGAAGAGGCTTCTGACGTGGTCCGTCAAAAGAAGAAGCACCCCAAGAAGCCTAAGGCAGAGGCTGTGCT
AGCCCCGCCGCAGCCCACTCCTGAGACAGTGCCTGTGATCAATAAGAGTGACATTAAGCAATATGACTTTCAGAGCTCAG
ATGAAGATGAATTTCCACAGGTACCATCTCCATCATCAGAACCTGAAGAAGAAAATGATCCTGATGGTCCCTGTGCTTTC
AGAAGGCGGGCAGGATGCCAGTATTATGCTCCGCGTTTGGACCAAGCTAATAACCATCCGTGCAAAAGTTCAGAGTTGGC
AGACTTGGATAAGTTGAGGTATAAGCATTGTCTCACAACACTTACAGTTCCAAGAAGATGTATAGGGTTTGCCAGGAGGC
GAATTGGCAGGGGTGGAAGGGTCATAATGGACCGAATATCCACAGAACATGACCCCGTCCTAAAACAGATAGACCCTGAG
ATGCTGAATGGGCTTTCAAGCTCTTCCCAAACTATAGACTTTTCTTCTAATTTCTCTCGGACCAATGCTTCCAGTAAACC
TTGTGAAAATAGACTGTCCCTTTCTGAAATATTAAGCAATATCAGATCATGTCGACTACAGTGTTTCCAGCCAAGGCTAC
TAAATGTACAGGACATTGATAGTGAAGAATATACCTCAAGAAAACCAGGGCAGACTGTGAGCAGTAAAAGGGTTTCTGCA
GCATCTGTAGCTTTATTGAACACCAGCAAGAACGGCATATCAGTCACAGGGGGCATCACAGAAGAGCAGTTTCAGACACA
TCAACAGCAGCTAGCTCAAATGCAAAGGCAGCAACTCGCGCAGCTTCAGCAGAAACAGCAATCCCAGCATTCCTCACAGC
AGACACATCCAAAAGCACAGGGCTCAAGCACCTCGGACTGTATGTCTAAAACACTTGACTCAGCCAGCGCCCACTTTGCT
GCATCTGCAGTGGTCAGTGCTCCTGTTCCAAGTCGCAGTGAGGGATCTAAGGAACAGAACACTGGCCACAACAATATGAA
TGGTGTTGTCCAGCCTTCAGGACCCTCTAAAACATTATATTCCACCAATATGGCTTTATCATCCAGCCCAGGGATTTCAG
CTGTACAGCTTGTAAGGACAGTTGGCCACACTACTACAAACCACTTGATCCCAGCGTTGTGCACAAGCAGTCCTCAGACA
CTTCCCATGAACAATTCCTGCCTGACCAATGCAGTGCACCTCAATAATGTCAGTGTTGTTTCTCCTGTCAATGTGCATAT
CAATACACGGACTTCAGCACCATCGCCAACAGCCTTAAAACTTGCCACAGTTGCTGCCAGTATGGACAGAGTGCCAAAGG
TTACTCCCAGCAGTGCCATCAGCAGCATAGCCAGAGAGAACCATGAACCAGAAAGACTGGGTTTAAATGGAATAGCAGAG
ACAACAGTAGCTATGGAAGTGACA
ORF - retro_rnor_588 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.13 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSKLSFRARALDAAKPLPIYRGKDMPDLNDCVSINRAVPQMPTGMEKEEESEHHLQRAISAQQVFREKKE |
| MSKLSFRARALDAAKPLPIYRGKDMPDLNDCVSINRAVPQMPTGMEKEEESEHHLQRAISAQQVFREK.E | |
| Retrocopy | MSKLSFRARALDAAKPLPIYRGKDMPDLNDCVSINRAVPQMPTGMEKEEESEHHLQRAISAQQVFREKNE |
| Parental | SMVIPVPEAESNVNYYNRLYKGEFKQPKQFIHIQPFNLDNEQPDYDMDSEDETLLNRLNRKMEIKPLQFE |
| SMVIPVPEAESNVNYYNRLYKGEFKQPKQFIHIQPFNLDNEQPDYDMDSEDETLLNRLNRKME.KPLQFE | |
| Retrocopy | SMVIPVPEAESNVNYYNRLYKGEFKQPKQFIHIQPFNLDNEQPDYDMDSEDETLLNRLNRKMEVKPLQFE |
| Parental | IMIDRLEKASSNQLVTLQEAKLLLNEDDYLIKAVYDYWVRKRKNCRGPSLIPQIKQEKRDGSTNNDPYVA |
| IMIDRLEKASSNQLVTLQEA.LLLNEDDYLIKAVYDYWVRK.KNCRGPSLIPQIKQEKRDGSTNNDPYVA | |
| Retrocopy | IMIDRLEKASSNQLVTLQEAELLLNEDDYLIKAVYDYWVRKSKNCRGPSLIPQIKQEKRDGSTNNDPYVA |
| Parental | FRRRTEKMQTRKNRKNDEASYEKMLKLRREFSRAITILEMIKRREKTKRELLHLTLEVVEKRYHLGDYGG |
| FRRRTEKMQTRKNRKNDEASYEKMLKLRREFSRAITILEMIKRREKTKRELLHLTLEVVEKRYHLGDYGG | |
| Retrocopy | FRRRTEKMQTRKNRKNDEASYEKMLKLRREFSRAITILEMIKRREKTKRELLHLTLEVVEKRYHLGDYGG |
| Parental | EILNEVKVNRSEKELYASPATLHNGNHHKVQECKTKHPHHLSLKEEASDVVRQKKKHPKKPKAEAVLAPP |
| EILNEVKVNRSEKELYASPATLHNGNHHKVQECKTKHPHHLSLKEEASDVVRQKKKHPKKPKAEAVLAPP | |
| Retrocopy | EILNEVKVNRSEKELYASPATLHNGNHHKVQECKTKHPHHLSLKEEASDVVRQKKKHPKKPKAEAVLAPP |
| Parental | QPTPETVPVINKSDIKQYDFQSSDEDEFPQVPSPASEPEEENDPDGPCAFRRRAGCQYYAPRLDQANNHP |
| QPTPETVPVINKSDIKQYDFQSSDEDEFPQVPSP.SEPEEENDPDGPCAFRRRAGCQYYAPRLDQANNHP | |
| Retrocopy | QPTPETVPVINKSDIKQYDFQSSDEDEFPQVPSPSSEPEEENDPDGPCAFRRRAGCQYYAPRLDQANNHP |
| Parental | CESSELADLDKLRYKHCLTTLTVPRRCIGFARRRIGRGGRVIMDRISTEHDPVLKQIDPEMLNGLSSSSQ |
| C.SSELADLDKLRYKHCLTTLTVPRRCIGFARRRIGRGGRVIMDRISTEHDPVLKQIDPEMLNGLSSSSQ | |
| Retrocopy | CKSSELADLDKLRYKHCLTTLTVPRRCIGFARRRIGRGGRVIMDRISTEHDPVLKQIDPEMLNGLSSSSQ |
| Parental | TIDFSSNFSRTNASSKPCENRLSLSEILSNIRSCRLQCFQPRLLNVQDIDSEECTSRKPGQTVSSKRVSA |
| TIDFSSNFSRTNASSKPCENRLSLSEILSNIRSCRLQCFQPRLLNVQDIDSEE.TSRKPGQTVSSKRVSA | |
| Retrocopy | TIDFSSNFSRTNASSKPCENRLSLSEILSNIRSCRLQCFQPRLLNVQDIDSEEYTSRKPGQTVSSKRVSA |
| Parental | ASVALLNTSKNGISVTGGITEEQFQTHQQQLAQMQRQQLAQLQQKQQSQHSSQQTHPKAQGSSTSDCMSK |
| ASVALLNTSKNGISVTGGITEEQFQTHQQQLAQMQRQQLAQLQQKQQSQHSSQQTHPKAQGSSTSDCMSK | |
| Retrocopy | ASVALLNTSKNGISVTGGITEEQFQTHQQQLAQMQRQQLAQLQQKQQSQHSSQQTHPKAQGSSTSDCMSK |
| Parental | TLDSASAHFAASAVVSAPVPSRSEGSKEQNTGHNNMNGVVQPSGPSKTLYSTNMALSSSPGISAVQLVRT |
| TLDSASAHFAASAVVSAPVPSRSEGSKEQNTGHNNMNGVVQPSGPSKTLYSTNMALSSSPGISAVQLVRT | |
| Retrocopy | TLDSASAHFAASAVVSAPVPSRSEGSKEQNTGHNNMNGVVQPSGPSKTLYSTNMALSSSPGISAVQLVRT |
| Parental | VGHTTTNHLIPALCTSSPQTLPMNNSCLTNAVHLNNVSVVSPVNVHINTRTSAPSPTALKLATVAASMDR |
| VGHTTTNHLIPALCTSSPQTLPMNNSCLTNAVHLNNVSVVSPVNVHINTRTSAPSPTALKLATVAASMDR | |
| Retrocopy | VGHTTTNHLIPALCTSSPQTLPMNNSCLTNAVHLNNVSVVSPVNVHINTRTSAPSPTALKLATVAASMDR |
| Parental | VPKVTPSSAISSIARENHEPERLGLNGIAETTVAMEVT |
| VPKVTPSSAISSIARENHEPERLGLNGIAETTVAMEVT | |
| Retrocopy | VPKVTPSSAISSIARENHEPERLGLNGIAETTVAMEVT |
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 .72 RPM | 17 .69 RPM |
| SRP017611_kidney | 0 .35 RPM | 8 .30 RPM |
| SRP017611_liver | 0 .07 RPM | 4 .03 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_588 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_588 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_588 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 | ENSRNOG00000029447 | 1 retrocopy |
retro_rnor_588 ,
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