RetrogeneDB ID: | retro_rnor_1123 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 15:84428904..84429299(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
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_1123
GAATCAGAAATTGTGGAATGTATCATGAAATAGCTATAACACATGGCAGAAAATCCTAGAAGAGACAAAAGCCTTGATCT
GAAGGTCAGAACTTATCAAAGAGAGACGGACAGCATCTCTTATATCCTTGGCAGCTACTTGCAGTGTTGATTCATGAAGA
TAGAGAACTTTTTCCTCTACATCCCAGAAAAGGAGAAAATGTGTCCTGGGGTGGCTGGGAGGCCTCTAGCCTTTGTGCAG
AGAAATTTATCTTTGCCATGGTTCACATAGAGATCTATCTTAAAAACATTTCCTCAAACGACATGCCGCCCAATCTTCAG
AAAGTGGACCTCTTAAAGGCAGTTCCCAAAGCAGATTTAGGGTCACACGTGTTTGGGGGAGTGCAAGAATGACAA
ORF - retro_rnor_1123 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 55.15 % |
| Parental protein coverage: | 59.64 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | KSEIVECVVEQLEHMEENLRRAKKGDLKVSIHRMEMERIRYVLSSYLRCRLMKIEKFFPHILEKEKTRP- |
| .SEIVEC....L.HM.EN.RR.K..DLKV.....E...I.Y.L.SYL.C..MKIE.FF..I.EKEK..P. | |
| Retrocopy | ESEIVECIMK*L*HMAENPRRDKSLDLKVRTYQRETDSISYILGSYLQC*FMKIENFFLYIPEKEKMCPG |
| Parental | -AGEP-SSLSPEEFVFAKEYMDHTETHFKNVALKHMPPNLQKVDLMRAVPKPDLDSYVFLRVKERQ |
| .AG.P.SSL..E.F.FA...M.H.E...KN.....MPPNLQKVDL..AVPK.DL.S.VF..V.E.Q | |
| Retrocopy | VAGRP<SSLCAEKFIFA---MVHIEIYLKNISSNDMPPNLQKVDLLKAVPKADLGSHVFGGVQE*Q |
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_1123 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_1123 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_1123 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,
|