RetrogeneDB ID: | retro_rnor_678 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 10:29924619..29924956(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSRNOG00000027881 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Gins4 | ||
| Ensembl ID: | ENSRNOG00000018040 | ||
| Aliases: | Gins4, 2810037c03rik, RGD1307397 | ||
| Description: | DNA replication complex GINS protein SLD5 [Source:RefSeq peptide;Acc:NP_001025198] |
Retrocopy-Parental alignment summary:
>retro_rnor_678
AGCTATTTGTGGTGTCAACTCATGAAGATAGAGAAGTTTTTCCCTCACATCCTAGAAAAGGAGAAAACACACCCTGCAGG
AGAGCCTTCCAGCCCGTCTCCAGGGGAAGTTTGTCTTTGCCAAAGAGTATATGGATCACACAGAGACCCATTTTAAAAAT
GTTGCCTTAAAGCACATGCCTCCCAAGCTGCAGAAAGTGGACCTCATGAGGGCAGTTCCCGAACCAGACCTAGAGTCATA
CGTGTTTCTGAGAGTGAAAGAGCGACAGGAAAACATACTAGTAGAACCCGAAGCTGATGAGCAGAGAGACTATGCTATTG
ACTTGGAGGAGGGCTCT
ORF - retro_rnor_678 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.15 % |
| Parental protein coverage: | 50.22 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | SYLRCRLMKIEKFFPHILEKEKTRPAGEPSSLSPEE-FVFAKEYMDHTETHFKNVALKHMPPNLQKVDLM |
| SYL.C.LMKIEKFFPHILEKEKT.PAGEPSS.SP.E.FVFAKEYMDHTETHFKNVALKHMPP.LQKVDLM | |
| Retrocopy | SYLWCQLMKIEKFFPHILEKEKTHPAGEPSSPSPGE>FVFAKEYMDHTETHFKNVALKHMPPKLQKVDLM |
| Parental | RAVPKPDLDSYVFLRVKERQENILVEPEADEQRDYVIDLEEGS |
| RAVP.PDL.SYVFLRVKERQENILVEPEADEQRDY.IDLEEGS | |
| Retrocopy | RAVPEPDLESYVFLRVKERQENILVEPEADEQRDYAIDLEEGS |
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 | 1 .87 RPM |
| SRP017611_kidney | 0 .00 RPM | 1 .74 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .61 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_678 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_678 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_678 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Rattus norvegicus | ENSRNOG00000018040 | 2 retrocopies |
retro_rnor_1123, retro_rnor_678 ,
|