RetrogeneDB ID: | retro_rnor_2250 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 5:126960688..126961506(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ndufs2 | ||
| Ensembl ID: | ENSRNOG00000038372 | ||
| Aliases: | None | ||
| Description: | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q641Y2] |
Retrocopy-Parental alignment summary:
>retro_rnor_2250
ATGGACATTGGTGCCATGACTCCATTCTTTTGGATGGTTGAGGAAAAGAGAATATGTTCAAGGTCTATGAGTGGGTGTCT
GGAGCCCGAATGCATACTGCTTGTATCCGACAAGGAGGAGTATACCAGGACCTATATTTTAGGCTTATGGATAACTTTTA
TGAATTTTCCAAGAACTTCTCTCTTTGAATTGATGAGGTGTAAGAGATGCTGACCAACAATAGAATCTGGCAAAATAGGA
CAGTTGACATTGGAGATGTATCAGCAGAAGACGCACTTAACTATGGATTCAGTGAGGTGATACTCCAAGGCTCAGGCATC
TAGTGGGTCTTGCAGAAGACCCAGCCCTATGATGTTTACAGCCAGGTCAAGTTTGATTCCTGTTCCTGTTGGTCTCAAGG
GGCCTGCTATAATAAGTACCTCTGTCACAAGGAGAAGATGTGCCAGTCCCTTCAAATCATTGAACAGTGTCTGAACAAGA
TGCCTCTGGGGGAGATCAAGGTTGATTATGCCAAAGTGTTCTTACCTAAGCAAGCAGAGATGAAGACTTTCATGAAGTCA
CCAATCCATCACTTTAAGCTGTATACTGAGGGTTACCAAGTTCCTCCAGGAACCACGTATACTATGACTGAAGCTCCTAA
GGGAGAGTTGGGGTATACTTGGTGTCTGATAGCAAGCAGCCACTCTTATCAGTGTAAGTTCAAGGCTCTTGGGTTTGCCC
GCCTTGCTGGTTTGGAGAAGATGTCTGAGGGACACATGTTAGCAGGCATCATAGCCATCATAGGTACCCAGAATATTGTT
TTTGGAGAAATAAACCAA
ORF - retro_rnor_2250 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.91 % |
| Parental protein coverage: | 58.75 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | LDIGAMTPFFWMFEER-EKMFEFYERVSGARMHAAYIRPGGVHQDLPLGLMDDIYEFSKNFSLRIDEVEE |
| .DIGAMTPFFWM.EE..E.MF..YE.VSGARMH.A.IR.GGV.QDL...LMD..YEFSKNFSL.IDEV.E | |
| Retrocopy | MDIGAMTPFFWMVEEK<ENMFKVYEWVSGARMHTACIRQGGVYQDLYFRLMDNFYEFSKNFSL*IDEV*E |
| Parental | MLTNNRIWRNRTVDIGVVSAEDALNYGFSGVMLRGSGIQWDLRKTQPYDVYDQVEFD-VPIGSRGDCYDR |
| MLTNNRIW.NRTVDIG.VSAEDALNYGFS.V.L.GSGI.W.L.KTQPYDVY.QV.FD.....S.G.CY.. | |
| Retrocopy | MLTNNRIWQNRTVDIGDVSAEDALNYGFSEVILQGSGI*WVLQKTQPYDVYSQVKFDSCSCWSQGACYNK |
| Parental | YLCRVEEMRQSLRIIEQCLNKMPPGEIKVDDAKVSPPKRAEMKTSMESLIHHFKLYTEGYQVPPGATYTA |
| YLC..E.M.QSL.IIEQCLNKMP.GEIKVD.AKV..PK.AEMKT.M.S.IHHFKLYTEGYQVPPG.TYT. | |
| Retrocopy | YLCHKEKMCQSLQIIEQCLNKMPLGEIKVDYAKVFLPKQAEMKTFMKSPIHHFKLYTEGYQVPPGTTYTM |
| Parental | IEAPKGEF-GVYLVSD-GSSRPYRCKIKAPGFAHLAGLDKMSKGHMLADVVAIIGTQDIVFGEIDR |
| .EAPKGE..GVYLVSD..SS..Y.CK.KA.GFA.LAGL.KMS.GHMLA...AIIGTQ.IVFGEI.. | |
| Retrocopy | TEAPKGEL<GVYLVSD>ASSHSYQCKFKALGFARLAGLEKMSEGHMLAGIIAIIGTQNIVFGEINQ |
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 | 142 .93 RPM |
| SRP017611_kidney | 0 .00 RPM | 248 .49 RPM |
| SRP017611_liver | 0 .00 RPM | 130 .04 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2250 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2250 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2250 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 | |
|---|---|---|---|
| Echinops telfairi | ENSETEG00000015746 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000038372 | 1 retrocopy |
retro_rnor_2250 ,
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