RetrogeneDB ID: | retro_rnor_656 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 1:255297392..255298872(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Trmt6 | ||
| Ensembl ID: | ENSRNOG00000021270 | ||
| Aliases: | Trmt6, RGD1308877 | ||
| Description: | tRNA (adenine-N(1)-)-methyltransferase non-catalytic subunit TRM6 [Source:RefSeq peptide;Acc:NP_001101249] |
Retrocopy-Parental alignment summary:
>retro_rnor_656
ATGGAGATGTCAGACGCGGAGCAGCCGAGCCCACAGCCCCCGCATCTCGGGGACCACTGCATCCATGACGGCGACTTCGT
GGTGCTGAAGCGAGAAGATGTGTTCGAAGCAGTGCAAGTCCAGCGGAGGAAAAAAGTAACTTTTGAAAAACAGTAGTTCT
ACCTGGATAACGCCATTGGCCATAGTTACGGGTCAACGTTTGAAGTGAGCAGTGGAGGAAGCCTTCAGCTCAGGAAGAAG
CTGGAAGAGCCCACGTCAGAGACCAAAGAAGGGGGCACTGATAATCGAAACATAGTTGATGATGGAAAGTCCCAGAAACT
TACTCAAGATGATATAAAGGCTCTGAAAGACAAGGGCATTAAAGGAGAGGAAATACTTCAGCAGCTAATTGAAAATAGTA
CATTTCGAGACGAGACAGAATTTGCTCAAGATAAATATATTAAAAAGAAGAAAAAAAATGAAGCTATCATTACTATTTTG
AAGCCATCTACCTGTATTCTTTCAATTATGTATTATGAAAGAGAACCTGGAAAAATTAACCACATGAGATATGATACACT
AGCCCAGATGTTGACGTTGGGAAATATCTGTGCTGGCAATAAAATGATTGTCATGGAAACATGTTCAGGCTTGGTGCTAG
GAGCCATGATGGAATGAATGGAAGGCTTTGGCTCCATTGTTCAGCTGTACCCTGGAGATGGACCCGTTTTGGGCAGCAAC
AGCTTGTTTTGGATTTCCCAAATCTTTCCCCAGTGGTCTTCATGAATTTCCCCTCAACAAAGTAAAAAGTCTCCTCAGTG
GAACATTTTCTGCCGAAATGCTATCCTCAGAGCCTAGAGACAGCACTGCAGTTAAAGAAAGTAATGGTGAGCTTGAGAAA
GAGATTGCTGAACAGGCGGATAAGGACAGCATTGCAGACGGCCCAGAAGGCAACGCAGAACAGAGCCCCGTGGACATTGT
TCCTGGGGTCCCAGAGAGTAAGGAGCCTAAAGAAAAAGAAGCAAAAGAGATTATATTCAGGAAAAACAAAGGAGACAAGA
AGAGCAGAGGAAAAGACATGTGGAGGTTGCTGCTCTGCTGGGAGAAAGAAATGCAGATGGTTTGATCGTGGCCAGTCGTT
TCCACCCCACGCCCCTGCTGCTGTCTTTGCTGGACTTTGTAGCCGGTCAAGGCCGCGGTTTGTGGTCTATTGTCAGTATA
AAGAGCCTTTGTTGGAATGTTACACAAAACTGTGGGAGAGGGGAGGAGTCATTAACCTAAGACTGTCTGAAACCTGGCTC
AGAAATTACCAGGTTCTGCTAGACGGAGTCATCCCGAATTGTTGATGAGTGGAGGTAGAGGGTACCTTCTGTCAGGCTTC
ACTGTTGTCTCAAACAGCCATCGAGTAGACCCCAGTCTCGAGTCCTGTGAGGGTGCTTTACACTCACCCAAGACTGAGGA
GCCAGCAGCTAAGAAACAGAAATGCATGGAATCTGCCTCT
ORF - retro_rnor_656 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.6 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | MELSAAEQPSPQPPHLGDHCIHDGDFVVLKREDVFKAVQVQRRKKVTFEKQWFYLDNAIGHSYGSTFEVS |
| ME.S.AEQPSPQPPHLGDHCIHDGDFVVLKREDVF.AVQVQRRKKVTFEKQ.FYLDNAIGHSYGSTFEVS | |
| Retrocopy | MEMSDAEQPSPQPPHLGDHCIHDGDFVVLKREDVFEAVQVQRRKKVTFEKQ*FYLDNAIGHSYGSTFEVS |
| Parental | SGGSLQLRKKLEEPTSETKEAGTDNRNIVDDGKSQKLTQDDIKALKDKGIKGEEIVQQLIENSTTFRDKT |
| SGGSLQLRKKLEEPTSETKE.GTDNRNIVDDGKSQKLTQDDIKALKDKGIKGEEI.QQLIENS.TFRD.T | |
| Retrocopy | SGGSLQLRKKLEEPTSETKEGGTDNRNIVDDGKSQKLTQDDIKALKDKGIKGEEILQQLIENS-TFRDET |
| Parental | EFAQDKYIKKKKKKYEAIITILKPSTRILSIMYYAREPGKINHMRYDTLAQMLTLGNIRAGNKMIVMETC |
| EFAQDKYI.......EAIITILKPST.ILSIMYY.REPGKINHMRYDTLAQMLTLGNI.AGNKMIVMETC | |
| Retrocopy | EFAQDKYI-XXXXXXEAIITILKPSTCILSIMYYEREPGKINHMRYDTLAQMLTLGNICAGNKMIVMETC |
| Parental | SGLVLGAMMERMGGFGSIIQLYPGDGPVR-AATACFGFPKSFLSGLHEFPLNKVKSLLNGTFSAEMLSSE |
| SGLVLGAMME.M.GFGSI.QLYPGDGPV..AATACFGFPKSF.SGLHEFPLNKVKSLL.GTFSAEMLSSE | |
| Retrocopy | SGLVLGAMME*MEGFGSIVQLYPGDGPVL>AATACFGFPKSFPSGLHEFPLNKVKSLLSGTFSAEMLSSE |
| Parental | PKDSTPVKESNGELEKEIAEQADKDSIADGPESNAEQNPVDIVPGDPESKEPKE-KGSKRDYIQEKQRRQ |
| P.DST.VKESNGELEKEIAEQADKDSIADGPE.NAEQ.PVDIVPG.PESKEPKE.K.SKRDYIQEKQRRQ | |
| Retrocopy | PRDSTAVKESNGELEKEIAEQADKDSIADGPEGNAEQSPVDIVPGVPESKEPKE<KRSKRDYIQEKQRRQ |
| Parental | EEQRKRHMEAAALLGERNADGLIVASRFHPTPLLLSLLDFVA-PSRP-FVVYCQYKEPLLECYTKLRERG |
| EEQRKRH.E.AALLGERNADGLIVASRFHPTPLLLSLLDFVA..SRP.FVVYCQYKEPLLECYTKL.ERG | |
| Retrocopy | EEQRKRHVEVAALLGERNADGLIVASRFHPTPLLLSLLDFVA<RSRPRFVVYCQYKEPLLECYTKLWERG |
| Parental | GVINLRLSETWLRNYQVLPD-RSHPKLLMSGGGGYLLSGFTVVSDSHRVDPSLKSCASALDSPKTEEPAA |
| GVINLRLSETWLRNYQVL.D.RSHP.LLMSGG.GYLLSGFTVVS.SHRVDPSL.SC..AL.SPKTEEPAA | |
| Retrocopy | GVINLRLSETWLRNYQVLLD<RSHPELLMSGGRGYLLSGFTVVSNSHRVDPSLESCEGALHSPKTEEPAA |
| Parental | KKQKCMESAS |
| KKQKCMESAS | |
| Retrocopy | KKQKCMESAS |
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 | 15 .10 RPM |
| SRP017611_kidney | 0 .00 RPM | 12 .35 RPM |
| SRP017611_liver | 0 .00 RPM | 6 .99 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_656 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_656 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_656 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 | ENSRNOG00000021270 | 1 retrocopy |
retro_rnor_656 ,
|
| Ictidomys tridecemlineatus | ENSSTOG00000006863 | 1 retrocopy |