RetrogeneDB ID: | retro_rnor_1654 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 2:158629987..158630477(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Samd3 | ||
| Ensembl ID: | ENSRNOG00000039955 | ||
| Aliases: | None | ||
| Description: | sterile alpha motif domain-containing protein 3 [Source:RefSeq peptide;Acc:NP_001165587] |
Retrocopy-Parental alignment summary:
>retro_rnor_1654
CATTCAGCTGTCCTTGACAATAGACTCATTTACCAAAGAGTGTTGGAGCAGAGAAGAAATGTAAAACATGTTCTAGCAAG
GCATAAAGCATAACAGTGGACTAAGTCCTCCATCTTACCGAATTTTCCCTATGATGTCAAGTGCATGTTAGCAGAGTAGA
AGCTCCTCAACCATAGCATTTGGATAAGGATCATTGAGTTTCTCCAGACAGATCTGCCTAAGTACCTGGAAGGCTCGCTG
TACCCTACCACCCAGCAATACAACGATGTGGTCAATGCTCTGCTGCAGCTCACCCTTTCCTGGATAAGGACAGTTGTTGC
TTTTTTTGGGGTGGAGGAAATGAACCCTCAAAGATCACTTTAAGTATGTCCAAAGAACCATAGAAGATGATGAACAAGTC
ATGACAAATAAGGGTAAATTTGGACACCGAAGAAGCCAGACAAGGAAATCTTTTGCTGACTTAAGATCTAATGAAATTAA
AATTGTGCAG
ORF - retro_rnor_1654 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.71 % |
| Parental protein coverage: | 59.34 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | YPAVLDNRLIDQRVLKQRRNVKHVLARHKALHWTKSYVLPEFPYDVKCVLAEQKRPDHSMRIRIIEFLQA |
| ..AVLDNRLI.QRVL.QRRNVKHVLARHKA..WTKS..LP.FPYDVKC.LAE.K...HS..IRIIEFLQ. | |
| Retrocopy | HSAVLDNRLIYQRVLEQRRNVKHVLARHKA*QWTKSSILPNFPYDVKCMLAE*KLLNHSIWIRIIEFLQT |
| Parental | DMTKYLEGSLYPTTQQYNDVVNALLQ-AHPFLDEDGCGF-FL-WKR-ALKDRFKYVRRPIEDDEQVMRNK |
| D..KYLEGSLYPTTQQYNDVVNALLQ.AHPFLD.D.C.F.FL.W....LKD.FKYV.R.IEDDEQVM.NK | |
| Retrocopy | DLPKYLEGSLYPTTQQYNDVVNALLQ<AHPFLDKDSCCF<FLGWRK*TLKDHFKYVQRTIEDDEQVMTNK |
| Parental | CKFGHRRGQTRKSLADIRSNEIKIVQ |
| .KFGHRR.QTRKS.AD.RSNEIKIVQ | |
| Retrocopy | GKFGHRRSQTRKSFADLRSNEIKIVQ |
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 .13 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_1654 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_1654 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_1654 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Rattus norvegicus | ENSRNOG00000039955 | 1 retrocopy |
retro_rnor_1654 ,
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