RetrogeneDB ID: | retro_rnor_1393 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 18:35760415..35761126(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ppp2r2d | ||
| Ensembl ID: | ENSRNOG00000016940 | ||
| Aliases: | None | ||
| Description: | Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform [Source:UniProtKB/Swiss-Prot;Acc:P56932] |
Retrocopy-Parental alignment summary:
>retro_rnor_1393
ATAGAAGCTTCACCTGCTAACATGGAGGAGCTGACAGAAGTCATCACTGCCGCGGAGTTCCACCCACACCAGTGCAATGT
ATTCGTCTACAGCAGCAGCAAGGGGACCATCAGGCTGTGTGACATGCGTTCTTCTGCCCTCTGTGATAGGCATGCCAAGT
TTTTTGAAGAGCCAGAAGATCCCAGCAGTAGATCCTTTTCCTCAGAAATAATCTCATCTATATCTGATGTCAAGTTCAGC
CACAGTGGTCGATACATGATGACCAGAGACTATCTGTCGGTGAAGGTATGGGACCTCAACATGGAGGGCAGGCCTGTCGA
GACCCACCAGGTACATGAGTACCTATGAAGCAAGCTCTGCTCCTTGTATGAGAATGACTGCATCTTTGACAAGTTCGAGT
GCTGCTGGAATGGTTCAGACAGTGCCATTATGACGGGGTCCTACAACAACTTCTTTAGAATGTTTGATAGAAACACTCGG
AGGGATGTTACACTGGAAACCTCAAGAGAGAACAGCAAGCCCCGAGCCAGCCTGAAGCCCCGGAAAGTGTGTTCAGGGGG
TAAGAGGAAGAAGGATGAGATTAGCATGGACAGTTTGGACTTCAATAAGAAGATCCTTCACACAGCCTGGCACCCCATGG
AGAGCATTATTGCTGTAGCTGCCACCAATAACTTGTATATATTCCAGGACAAAATTAATTAAGGAACTGAC
ORF - retro_rnor_1393 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.2 % |
| Parental protein coverage: | 70.45 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | VDIKPANMEELTEVITAAEFHPHQCNVFVYSSSKGTIRLCDMRSSALCDRHAKFFEEPEDPSSRSFFSEI |
| ....PANMEELTEVITAAEFHPHQCNVFVYSSSKGTIRLCDMRSSALCDRHAKFFEEPEDPSSRSF.SEI | |
| Retrocopy | IEASPANMEELTEVITAAEFHPHQCNVFVYSSSKGTIRLCDMRSSALCDRHAKFFEEPEDPSSRSFSSEI |
| Parental | ISSISDVKFSHSGRYMMTRDYLSVKVWDLNMEGRPVETHQVHEYLRSKLCSLYENDCIFDKFECCWNGSD |
| ISSISDVKFSHSGRYMMTRDYLSVKVWDLNMEGRPVETHQVHEYL.SKLCSLYENDCIFDKFECCWNGSD | |
| Retrocopy | ISSISDVKFSHSGRYMMTRDYLSVKVWDLNMEGRPVETHQVHEYL*SKLCSLYENDCIFDKFECCWNGSD |
| Parental | SAIMTGSYNNFFRMFDRNTRRDVTLEASRENSKPRASLKPRKVCSGGKRKKDEISVDSLDFNKKILHTAW |
| SAIMTGSYNNFFRMFDRNTRRDVTLE.SRENSKPRASLKPRKVCSGGKRKKDEIS.DSLDFNKKILHTAW | |
| Retrocopy | SAIMTGSYNNFFRMFDRNTRRDVTLETSRENSKPRASLKPRKVCSGGKRKKDEISMDSLDFNKKILHTAW |
| Parental | HPMESIIAVAATNNLYIFQDKIN-GTD |
| HPMESIIAVAATNNLYIFQDKIN.GTD | |
| Retrocopy | HPMESIIAVAATNNLYIFQDKIN*GTD |
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 .07 RPM | 18 .33 RPM |
| SRP017611_kidney | 0 .00 RPM | 15 .00 RPM |
| SRP017611_liver | 0 .00 RPM | 5 .65 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_1393 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_1393 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_1393 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 | ENSRNOG00000016940 | 1 retrocopy |
retro_rnor_1393 ,
|
| Ictidomys tridecemlineatus | ENSSTOG00000012446 | 1 retrocopy |