RetrogeneDB ID: | retro_rnor_1559 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 2:194654486..194655749(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ftsj3 | ||
| Ensembl ID: | ENSRNOG00000009857 | ||
| Aliases: | None | ||
| Description: | pre-rRNA processing protein FTSJ3 [Source:UniProtKB/Swiss-Prot;Acc:Q5RJT2] |
Retrocopy-Parental alignment summary:
>retro_rnor_1559
TCACTGTATTACCGAACCTCAATCAAGGACTTCTTGTGAGCCGGCAATCCTGTTGACTTCCTCTCCAAGGCCAGCGAAAT
CTCAATAGATGATGCAGAGTTGGCACAACACCCAGCTACCACTGAAGATATCAGAGCGTGCTATCAGGACATCAAAGTGC
TGGGGCGCAAGGAACTTAGGTCTCTACTGAATTGGAGAACAAAGCTTTGACGATATGTGGCCAAGAAGCTAAAAGAGCAA
GCAAAGGCACTAGACATCAGCCTCAGCTCGAAAGAAGAGGTGATGAAGAAGAGTCAGCAGCTGAACAAAGCAGGCTTCAG
AGGAGGAAGAGGAGAAAGTGGAGGAAGAGCAGCTTAACCGGACTCTGGCAGAGATAAAAGCCCAAGAAGTGGCAGAACTG
AAGAGGAAGAAGAAAAAATTCCTTCGTGAACAAAGGAAGCAGCGGGAGCGTGTAGAGCTGAAGATGGATCTGCCTGGGGT
CTCCATTGAAGATGAGGGGGAGACAGGCGTGTTCTCCCTGCGAACCATCCGTGGTCAGCAGTTGTTAGAGGAAGTAACAC
AAGGAGACATGAATGCTGCAGACACCTTTCTGTCTGATTTGCCAAGGGATGACATCTATGTGTCAGATGCTGAGGACGAT
GATGATACTTCTCTGGAAAGTGACCTGGATCCAGAAGAGTTGGCAGGAGTCAGGACACAGTCGGATCAGAAGGAGAAGAA
GTGCTTGCAGTTTGCTCAAGTAGATGACAGCAAAGAGGAAGGAGAGAATCCATTGCTGGTACCACTAGAAGAAAAGGCAG
TGCTGTAGGAAGAGCAAGCTAGCCTGTGGTTCTCCAAGGACAGCAGTGGGATAGAGGATGATGCTGACGAAGCCCTGGAG
ATCAGTCAGGTGCAGCTGCTGTACAAGAGCCGTCAGAAGGAGCAGCAGTCAACTGACCCACCTCTGCCATCTACTAACTT
GAAGACTGAGAAGAAATCTTCCCAGAATGAGGTCCCTAAGGAGACAGAGGCTATCATTGACGCTGGAGGGGAGGACAGAG
ACAGCTCAGATAGTGACAGCAGCAGTAGTGAGGATGAAGACTATTGGAAAGTATTCTGTGGTAAGAAGCGAAGCTGTGGT
TCTAAGGCAGTTGAGGATGGGTTTGAGGTGTGCCTATTGAGGACCCAGTGAAATATCGAATTCTGGACCCTGAAGGCCTT
GCTCTAGGTGCTGTTATTGCCTCTTCCAAAAAGGCAAAGAGAGACCTTATAGATAACTCATTC
ORF - retro_rnor_1559 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.58 % |
| Parental protein coverage: | 51.39 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | TLYHRTSVTDFLRAANPVDFLSKASEISIDDKELAQHPATTEDIRACCQDIKVLGRKELRSLLNWRTKLR |
| .LY.RTS..DFL.A.NPVDFLSKASEISIDD.ELAQHPATTEDIRAC.QDIKVLGRKELRSLLNWRTKL. | |
| Retrocopy | SLYYRTSIKDFL*AGNPVDFLSKASEISIDDAELAQHPATTEDIRACYQDIKVLGRKELRSLLNWRTKL* |
| Parental | RYVAKKLKEQAKALDISLSSEEE-GDEEESAAE-TKQASEEEEEREEEEQLNRTLAEMKAQEVAELKRKK |
| RYVAKKLKEQAKALDISLSS.EE.GDEEESAAE.TKQA...........QLNRTLAE.KAQEVAELKRKK | |
| Retrocopy | RYVAKKLKEQAKALDISLSSKEE<GDEEESAAE<TKQAXXXXXXXXXXXQLNRTLAEIKAQEVAELKRKK |
| Parental | KKLLREQRKQRERVELKMDLPGVSIADEGETGMFSLRTIRGQQLLEEVTQGDMNAADTFLSDLPRDDIYV |
| KK.LREQRKQRERVELKMDLPGVSI.DEGETG.FSLRTIRGQQLLEEVTQGDMNAADTFLSDLPRDDIYV | |
| Retrocopy | KKFLREQRKQRERVELKMDLPGVSIEDEGETGVFSLRTIRGQQLLEEVTQGDMNAADTFLSDLPRDDIYV |
| Parental | SDAEDDDDTSLESDLDPEELAGVRTHSDQKEQKSLQFAQVDDSKEEEGENPLLVPLEEKAVLQEEQASLW |
| SDAEDDDDTSLESDLDPEELAGVRT.SDQKE.K.LQFAQVDDSK.EEGENPLLVPLEEKAVL.EEQASLW | |
| Retrocopy | SDAEDDDDTSLESDLDPEELAGVRTQSDQKEKKCLQFAQVDDSK-EEGENPLLVPLEEKAVL*EEQASLW |
| Parental | FSKDGFSGIDDDADEALEISQAQLLYKSRQKEQQPTDPPPPPTNLKTEKKSSQCQNEVPKETEAITDTGG |
| FSKD..SGI.DDADEALEISQ.QLLYKSRQKEQQ.TDPP.P.TNLKTEKKSS..QNEVPKETEAI.D.GG | |
| Retrocopy | FSKDS-SGIEDDADEALEISQVQLLYKSRQKEQQSTDPPLPSTNLKTEKKSS--QNEVPKETEAIIDAGG |
| Parental | EDRDSSDSDSSSSEDEDDWKVSRGKKRSRGSKADEDGFEV-VPIEDPVKYRILDPEGLALGAVIASSKKA |
| EDRDSSDSDSSSSEDED.WKV..GKKRS.GSKA.EDGFEV.VPIEDPVKYRILDPEGLALGAVIASSKKA | |
| Retrocopy | EDRDSSDSDSSSSEDEDYWKVFCGKKRSCGSKAVEDGFEV<VPIEDPVKYRILDPEGLALGAVIASSKKA |
| Parental | KRDLIDNSF |
| KRDLIDNSF | |
| Retrocopy | KRDLIDNSF |
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 | 24 .59 RPM |
| SRP017611_kidney | 0 .00 RPM | 25 .82 RPM |
| SRP017611_liver | 0 .00 RPM | 12 .78 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_1559 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_1559 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_1559 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 | ENSRNOG00000009857 | 1 retrocopy |
retro_rnor_1559 ,
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