RetrogeneDB ID: | retro_mmul_1939 | ||
Retrocopy location | Organism: | Rhesus macaque (Macaca mulatta) | |
| Coordinates: | 5:31043456..31044109(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LIMS2 | ||
| Ensembl ID: | ENSMMUG00000004179 | ||
| Aliases: | None | ||
| Description: | LIM and senescent cell antigen-like-containing domain protein 2 [Source:RefSeq peptide;Acc:NP_001252623] |
Retrocopy-Parental alignment summary:
>retro_mmul_1939
GGGCATCTCTACCAGCCTTGCCATATCGCGAGAAGGCCAAGGGCCTGGCACAAGTGTCTGGCACCTCAGCAGTGCCACTT
GGTCATTCATGAGCAGCCCCTCATGTTCAGGAACAGTGCCTGACACCCAGGCCACTTCAGCTGCATCCACTGTAGGAAGG
AGCTGACTGGCGAGGCCCATGAGCTGAAGGGTGAACTCTACTGCCTGCCCTGCATTTACAAGATGCTGTCCCTATTTTTA
GGGACTGCAGCCAGCCCATCAAGGGTCACGTAGTGAATACACTGGGCAAAGAGTGGTGGCATGCAGAGCTTTTTGCCCTG
AGCGTGAGAAGCCATTCCTGGGGCTCTGGCACTATGAGAAGAAGGGCCTGGCCTACTTTGAGATCCACTACAGCCAGCTC
TTTGGAACATCTGCAGCCATGAAGTCGGGTGACATGGTGTTGGTCCTCAACAAGGCCTGATGTGTGTGAACTGCTTCTCC
TGTTCCACCTGCAAAAGCAGGCTCACTCTGAAGATCAACTTTGTGGAGTTTGACATGAAGCCCGTGTGTAAAAGGTGCTA
GATAACTTCCTCCTGGAGCTGAAGAAGAGGCTGAAGAAGTCATTGGAACTCACATCTCACTAGGCCCAGCCCAAGTCTGG
GGACCTCAACTCT
ORF - retro_mmul_1939 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 59.73 % |
| Parental protein coverage: | 94.44 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | GHLCRPCHNREKAKGLGKYIC-QRCHLVIDEQPLMFRSDAYHPDHFNCTHCGKELTAEARELKGELYCLP |
| GHL..PCH.........K....Q.CHLVI.EQPLMFR..A.HP.HF.C.HC.KELT.EA.ELKGELYCLP | |
| Retrocopy | GHLYQPCHIARRPRAWHKCLAPQQCHLVIHEQPLMFRNSA*HPGHFSCIHCRKELTGEAHELKGELYCLP |
| Parental | CHDKM-GVPICGACRRPIEGRVVNAL-GKQWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYNQLFG-D |
| C..KM..VPI...C..PI.G.VVN.L.G.........C...EKPFLG..HYEKKGLAY.E.HY.QLFG.. | |
| Retrocopy | CIYKM<AVPIFRDCSQPIKGHVVNTL<GQRVVACRAFCPEREKPFLGLWHYEKKGLAYFEIHYSQLFG<N |
| Parental | VCYNCSHVIEGDVVSALNKAWCVSCFSCSTCNSKLTLKNKFVEFDMKPVCKRC-YEKFPLELKKRLKKLS |
| .C...SH......V.......CV.CFSCSTC.S.LTLK..FVEFDMKPVCKRC....F.LELKKRLKK.. | |
| Retrocopy | IC---SHEVG*HGVGPQQGLMCVNCFSCSTCKSRLTLKINFVEFDMKPVCKRC<LDNFLLELKKRLKKSL |
| Parental | ELTSRKAQPKAADLNS |
| ELTS..AQPK..DLNS | |
| Retrocopy | ELTSH*AQPKSGDLNS |
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 |
|---|---|---|
| SRP007412_brain | 0 .22 RPM | 6 .61 RPM |
| SRP007412_brain_prefrontal_cortex | 0 .08 RPM | 13 .49 RPM |
| SRP007412_cerebellum | 0 .13 RPM | 2 .78 RPM |
| SRP007412_heart | 0 .00 RPM | 105 .52 RPM |
| SRP007412_kidney | 0 .00 RPM | 15 .38 RPM |
| SRP007412_liver | 0 .04 RPM | 37 .41 RPM |
| SRP007412_testis | 0 .00 RPM | 4 .00 RPM |
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_1939 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_1939 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmul_1939 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 | |
|---|---|---|---|
| Macaca mulatta | ENSMMUG00000003146 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000004179 | 1 retrocopy |
retro_mmul_1939 ,
|
| Macaca mulatta | ENSMMUG00000007922 | 1 retrocopy |