RetrogeneDB ID: | retro_ecab_305 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 14:1085820..1086820(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PPP2R2A | ||
| Ensembl ID: | ENSECAG00000019205 | ||
| Aliases: | None | ||
| Description: | protein phosphatase 2, regulatory subunit B, alpha [Source:HGNC Symbol;Acc:9304] |
Retrocopy-Parental alignment summary:
>retro_ecab_305
ACCAATGATAAAACAATCAAAGTATGGAAAATCAGTGAAAGGGACAAAAGACCAGAAGTGCGTAAGTTGAAAGAGGAAGG
CAGAAGATAGAGACCCTACCACAGTCACTGTACTATGAACGCCAGTCTTGAGGCCCATGGATCTAATGGCTGAGGCCAGT
GCATGAATAATACTTGCCAATGCTCACACATATCACATCAACTCAACTTCTATTAATAGTGATTACGAAATCTATTTATC
TGCAGGTGATTTGCGGATTAATTTTTGGCATCTGGAAATTACAGGCAGGAGTTCTAATGTTGTGGACATGGAGCCTGCCA
ATATGGAAGAGCTAAGAGAGGTGACTGCAGCAGCAGAATTCCACGCAAACAGCCGTAACACATCAGTACACAGCAGCAGT
GAAGGAACTATTCGGTTATGTGACATGAGGGCATCTGCCCTCTGTGACAGGCACTCTAAACTGTTTGAAGAACCTGAAGA
TCCCAGTAACAGGTCTTTTTTTCCTGAAATCATCTCCTCTATTTCTGATGTAAAATTCAGCCATTGTGGTCAATATGTGA
TGACTAGAGACTATTTCTCAGTCAAAACTTGGGACTTAAATATGGAAAACAGGCCTTTGGGAACATACAAGGTGCATGAA
TACGTCAGAAGTAAACTTTGTTCACTGTATGAAAATGACTGCATATTTGACAAATCCGAATGTTGTTGGAATGGATCTGA
CAGTGTTGTCATGACTGGATCTTGCAATAATTTTGTCAGAATGTTTGACAGGAACACAAAGCGAGACATAACCCTAGAAG
CATCACGGAAAAACAACAAACCCCGCATGGTTCTGAAGCCACACAAAGTCTGTGCAAGTGGCAACGGAAAGAAGGATGAA
ATAAGTGTCGACAGCCTAGACTTCAGCAAGAAAATACTTCATACGGCCTGGCAGCCCAAGGAAAATATCACTGCTGTAGC
TACTACAAACGATCTGGATATATTTCAAGACAAGGTGAAT
ORF - retro_ecab_305 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.28 % |
| Parental protein coverage: | 79.52 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | TNDKTIKLWKISERDKRPEGYNLKEEDGRY-RDPTTVTTLRVPVFRPMDLMVEASPRRIFANAHTYHINS |
| TNDKTIK.WKISERDKRPE...LKEE.GR..RDPTTVT.L..PV.RPMDLM.EAS...I.ANAHTYHINS | |
| Retrocopy | TNDKTIKVWKISERDKRPEVRKLKEE-GRR>RDPTTVTVL*TPVLRPMDLMAEASA*IILANAHTYHINS |
| Parental | ISINSDYETYLSADDLRINLWHLEITDRSFNIVDIKPANMEELTEVITAAEFHPNSCNTFVYSSSKGTIR |
| .SINSDYE.YLSA.DLRIN.WHLEIT.RS.N.VD..PANMEEL.EV..AAEFH.NS.NT.V.SSS.GTIR | |
| Retrocopy | TSINSDYEIYLSAGDLRINFWHLEITGRSSNVVDMEPANMEELREVTAAAEFHANSRNTSVHSSSEGTIR |
| Parental | LCDMRASALCDRHSKLFEEPEDPSNRSFFSEIISSISDVKFSHSGRYMMTRDYLSVKIWDLNMENRPVET |
| LCDMRASALCDRHSKLFEEPEDPSNRSFF.EIISSISDVKFSH.G.Y.MTRDY.SVK.WDLNMENRP..T | |
| Retrocopy | LCDMRASALCDRHSKLFEEPEDPSNRSFFPEIISSISDVKFSHCGQYVMTRDYFSVKTWDLNMENRPLGT |
| Parental | YQVHEYLRSKLCSLYENDCIFDKFECCWNGSDSVVMTGSYNNFFRMFDRNTKRDITLEASRENNKPRTVL |
| Y.VHEY.RSKLCSLYENDCIFDK.ECCWNGSDSVVMTGS.NNF.RMFDRNTKRDITLEASR.NNKPR.VL | |
| Retrocopy | YKVHEYVRSKLCSLYENDCIFDKSECCWNGSDSVVMTGSCNNFVRMFDRNTKRDITLEASRKNNKPRMVL |
| Parental | KPRKVCASGKRKKDEISVDSLDFNKKILHTAWHPKENIIAVATTNNLYIFQDKVN |
| KP.KVCASG..KKDEISVDSLDF.KKILHTAW.PKENI.AVATTN.L.IFQDKVN | |
| Retrocopy | KPHKVCASGNGKKDEISVDSLDFSKKILHTAWQPKENITAVATTNDLDIFQDKVN |
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 |
|---|---|---|
| SRP021940_articular_cartilage | 0 .00 RPM | 15 .58 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 24 .20 RPM |
| SRP021940_embryo | 0 .03 RPM | 26 .75 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 24 .92 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 16 .28 RPM |
| SRP021940_testis | 0 .06 RPM | 22 .06 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_305 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_305 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_305 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000019205 | 1 retrocopy |
retro_ecab_305 ,
|
| Monodelphis domestica | ENSMODG00000016691 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000022052 | 1 retrocopy |