RetrogeneDB ID: | retro_rnor_2054 | ||
Retrocopylocation | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 4:40452909..40453203(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSRNOG00000049404 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_rnor_2054
CAGCAGATCAGGAACCTGATCAAAGATGGGCAGATCATCTGGAAGCCTGTTACTGTCCATTCCTGACTTTGATGCTGGGA
AAACATGCCTGTTGAAAGGACAGGTATATGGGCATAGGGAAACTGCCCACTCTCAGATGCCAGAGAAGGTGATCTGGATG
AGAATCTTGCACCATCTTCTCAAGAGATACAGAGAATCTAAGAAGATTGGCCACCTATGTATCACAACCTGTACCTGAAT
GTCAAAAGGAATGTATTAAAAAATGAGGAGGTTCTCATGTAGCACATCAACAAG
CAGCAGATCAGGAACCTGATCAAAGATGGGCAGATCATCTGGAAGCCTGTTACTGTCCATTCCTGACTTTGATGCTGGGA
AAACATGCCTGTTGAAAGGACAGGTATATGGGCATAGGGAAACTGCCCACTCTCAGATGCCAGAGAAGGTGATCTGGATG
AGAATCTTGCACCATCTTCTCAAGAGATACAGAGAATCTAAGAAGATTGGCCACCTATGTATCACAACCTGTACCTGAAT
GTCAAAAGGAATGTATTAAAAAATGAGGAGGTTCTCATGTAGCACATCAACAAG
ORF - retro_rnor_2054 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 56.73 % |
| Parental protein coverage: | 53.4 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | QLIRKLIEDGLIIWKPVTVH-PQTRCLKTLKGRHMVIGKGKGTANTWVPERVTWMRRMRILHRLLRRYWE |
| Q.IR.LI.DG.IIWKPVTVH.P.....KT......V.G....TA....PE.V.WMR...ILH.LL.RY.E | |
| Retrocopy | QQIRNLIKDGQIIWKPVTVH>PDFDAGKTCLLKGQVYGH-RETAHSQMPEKVIWMR---ILHHLLKRYRE |
| Parental | SKKIDH-HMYHSLYLKVKRNVFKNQWILMEQILK |
| SKKI.H..MYH.LYL.VKRNV.KN...LM..I.K | |
| Retrocopy | SKKIGH<PMYHNLYLNVKRNVLKNEEVLM*HINK |
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 | 0 .00 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .00 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2054 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2054 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2054 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 49 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Rattus norvegicus | ENSRNOG00000004741 | 37 retrocopies |
retro_rnor_1029, retro_rnor_1039, retro_rnor_1295, retro_rnor_1338, retro_rnor_1405, retro_rnor_1440, retro_rnor_1449, retro_rnor_1478, retro_rnor_1512, retro_rnor_1525, retro_rnor_1558, retro_rnor_1577, retro_rnor_1765, retro_rnor_1766, retro_rnor_1795, retro_rnor_1814, retro_rnor_1860, retro_rnor_1885, retro_rnor_1905, retro_rnor_1907, retro_rnor_1970, retro_rnor_1981, retro_rnor_208, retro_rnor_2169, retro_rnor_2522, retro_rnor_2536, retro_rnor_2708, retro_rnor_2773, retro_rnor_2783, retro_rnor_2921, retro_rnor_2943, retro_rnor_326, retro_rnor_426, retro_rnor_434, retro_rnor_464, retro_rnor_465, retro_rnor_829,
|
| Rattus norvegicus | ENSRNOG00000049404 | 12 retrocopies |