RetrogeneDB ID: | retro_rnor_562 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 1:6889415..6889973(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSRNOG00000014431 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Dctn3 | ||
| Ensembl ID: | ENSRNOG00000014208 | ||
| Aliases: | None | ||
| Description: | dynactin 3 [Source:RefSeq peptide;Acc:NP_001102129] |
Retrocopy-Parental alignment summary:
>retro_rnor_562
ATGGCGGCTCTGACCGATGTGCAGCGGCTACAGTCCCGAGTGGAGGAGCTGGAGCGCTGGGTGTATGGGCCAGGCGGGAC
CCGAGGCTCTAGGAAGGTAGCTGATGGTCTAGTCAAGGTGCAGGTGGCTTTAGGGAACATTGCCAGTAAGAGGGAGAGGG
TGAAGATTCTCTACAAAAAGATTGAAGTCCTGATCAAATACCTGGATCCTGAGTACATTGATCGCATTGCTATACCTGAG
GCCTCGAAGTTGCAGTTCATCTTGGCAGAGGAACAGTTCATCCTCTCCCAGGTGGCGCTCTTGGAACAAGTGAACACCTT
GGTGCCGGTGCTGGACAGCGCTTCTATCAAAGCCGTTCCTGAGCATGCTGCCCGCCTGCAGCGCTTGGCGCAGATCCACA
TCCAACAGCAGGACCAGTGTGTGGAGATCACTGAGGAGTCCAAGGCTCTCCTGGAGGAGTATAACAAGACTACAATGCTT
CTCTCCAAGCAGCTTGTGCAGTGGGACGAGCTACTCTGCCAGCTAGAGGCTGCCAAGCAAGTGAAGCCAGCAGCAGAA
ORF - retro_rnor_562 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.39 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAALTDVQRLQSRVEELERWVYGPGGTRGSRKVADGLVKVQVALGNIASKRERVKILYKKIEDLIKYLDP |
| MAALTDVQRLQSRVEELERWVYGPGGTRGSRKVADGLVKVQVALGNIASKRERVKILYKKIE.LIKYLDP | |
| Retrocopy | MAALTDVQRLQSRVEELERWVYGPGGTRGSRKVADGLVKVQVALGNIASKRERVKILYKKIEVLIKYLDP |
| Parental | EYIDRIAIPEASKLQFILAEEQFILSQVALLEQVNTLVPMLDSASIKAVPEHAARLQRLAQIHIQQQDQC |
| EYIDRIAIPEASKLQFILAEEQFILSQVALLEQVNTLVP.LDSASIKAVPEHAARLQRLAQIHIQQQDQC | |
| Retrocopy | EYIDRIAIPEASKLQFILAEEQFILSQVALLEQVNTLVPVLDSASIKAVPEHAARLQRLAQIHIQQQDQC |
| Parental | VEITEESKALLEEYNKTTMLLSKQFVQWDELLCQLEAAKQVKPAAE |
| VEITEESKALLEEYNKTTMLLSKQ.VQWDELLCQLEAAKQVKPAAE | |
| Retrocopy | VEITEESKALLEEYNKTTMLLSKQLVQWDELLCQLEAAKQVKPAAE |
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 .22 RPM | 32 .93 RPM |
| SRP017611_kidney | 0 .07 RPM | 20 .03 RPM |
| SRP017611_liver | 0 .00 RPM | 7 .46 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_562 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_562 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_562 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Oryctolagus cuniculus | ENSOCUG00000000358 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000014208 | 1 retrocopy |
retro_rnor_562 ,
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