RetrogeneDB ID: | retro_rnor_2136 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 5:29725801..29726467(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Wsb1 | ||
| Ensembl ID: | ENSRNOG00000012929 | ||
| Aliases: | None | ||
| Description: | WD repeat and SOCS box-containing 1 isoform 1 [Source:RefSeq peptide;Acc:NP_001036026] |
Retrocopy-Parental alignment summary:
>retro_rnor_2136
ATGGCCAGCTTTCCCCCAAGGGACAACGAGAAAGAGATCGTGAGGTCGCGCACTATAGAAGAACTTTCAACTCCAGCAGC
CCCTTTCGACAGGAAATGTGGTGGTGAAAACTGGACTGTTGCTTTTGCTCCAGATGGTTCATACTTTGCATGGTCACTAG
GATTTCATATAGTGAAGCTTGTCCTGTGGTCCCGGTGCCTTAAGAACTTTCTTTTGCATGGTTCCAAGAATGTTACCAAT
TCAAGCTGTCTAAAATTGGCAAGACAAAATAGTAATGGTGCTCAAAAAAATAAGCCCCGTGAACACGTTATAGACTGTGG
AGACATAGTCTGGAGTCTCGCTTTTGGGTCTTCAGTTCCAGAAAAACAGAGTCGTTGTGTTAATAGAGAATGGCATCGGT
TTTGATTTGGACAGGATCAGCTACTCCTTGCCACAGGATTAAATAATGGTCGCATCAAAATCTGGGATGTGTATACAGGA
AAACTCTTCCTTGATTTGGCAGACCACATTGAAGTGGTTAGAGACTTAACTTTCGCTCCAGGTGGGAGCTTACTCCTTTT
ATCAGCTTCAAGAGACAATATTCTTAGAGTGTGGGACCTGAAAGGTGATGGAAATATGAGTATTGTGGGGCCATCAGAAT
TGGGTGTACAGTTGTGCGTTTTCTCC
ORF - retro_rnor_2136 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 84.3 % |
| Parental protein coverage: | 52.97 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MASFPPRVNEKEIVRSRTIGELLAPAAPFDKKCGGENWTVAFAPDGSYFAWSQGYRIVKLVPWSQCLKNF |
| MASFPPR.NEKEIVRSRTI.EL..PAAPFD.KCGGENWTVAFAPDGSYFAWS.G..IVKLV.WS.CLKNF | |
| Retrocopy | MASFPPRDNEKEIVRSRTIEELSTPAAPFDRKCGGENWTVAFAPDGSYFAWSLGFHIVKLVLWSRCLKNF |
| Parental | LLHGSKNVTNSSCLKLARQNSNGGQKNKPREHIIDCGDIVWSLAFGSSVPEKQSRCVNIEWHRFRFGQDQ |
| LLHGSKNVTNSSCLKLARQNSNG.QKNKPREH.IDCGDIVWSLAFGSSVPEKQSRCVN.EWHRF.FGQDQ | |
| Retrocopy | LLHGSKNVTNSSCLKLARQNSNGAQKNKPREHVIDCGDIVWSLAFGSSVPEKQSRCVNREWHRF*FGQDQ |
| Parental | LLLATGLNNGRIKIWDVYTGKLLLNLVDHIEVVRDLTFAPDGSLLLVSASRDKTLRVWDLKDDGNMVKVL |
| LLLATGLNNGRIKIWDVYTGKL.L.L.DHIEVVRDLTFAP.GSLLL.SASRD..LRVWDLK.DGNM.... | |
| Retrocopy | LLLATGLNNGRIKIWDVYTGKLFLDLADHIEVVRDLTFAPGGSLLLLSASRDNILRVWDLKGDGNM-SIV |
| Parental | RGHQNWVYSCAFS |
| ......V..C.FS | |
| Retrocopy | GPSELGVQLCVFS |
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 | 93 .03 RPM |
| SRP017611_kidney | 0 .00 RPM | 86 .67 RPM |
| SRP017611_liver | 0 .00 RPM | 43 .50 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2136 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2136 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2136 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 | |
|---|---|---|---|
| Rattus norvegicus | ENSRNOG00000012929 | 1 retrocopy |
retro_rnor_2136 ,
|
| Rattus norvegicus | ENSRNOG00000018027 | 1 retrocopy |