RetrogeneDB ID: | retro_ocun_1629 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | GL018724:3420265..3421721(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TRMT1 | ||
| Ensembl ID: | ENSOCUG00000021934 | ||
| Aliases: | None | ||
| Description: | tRNA methyltransferase 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:25980] |
Retrocopy-Parental alignment summary:
>retro_ocun_1629
AGAAGTCTTTGTAGAGCCTGGTTTATGGAGGGGAAACCCCAAGCATCCCTGAATCCAGCAGCAATGGAGAAAGGCAAAAA
GCACTGCATGGAAGAGAGCCCACCTGAGAAAAAGTAAACAACACACTGAGGGGGCTGTGACAGCAGCCTCTCTCACCTCC
AATTAGGTCTTCTATCACCGTGTAGAAGAGTTTCATGGGGACCTGATGTAAGCTGTGATCACAGAGTTTGCTTGCATCAT
CTCGAGTCCAAAGGCCTTCAAATCAAGGTATCAGCTGGGAAGAACCTGAAGCAGGTGGTTGTGGACCTGTCAGAGCAAGA
TGAAGAAATGGCTGAATCAAAAAGGTATGGAAACCTGGGGCCTGGAGTCCAATCTTCAACAGCTGCTGCAGGGGTGATCT
GTGAGGGAGGCCTCTGGGTGCTCGAGGGCCTTGTGGCTTCTGGATACAATCCATTCAACTGACCCGAAAGGTGCTGGAGC
CCCAATCTGTAGTTACCAACAATGGCTCTGCTAAGGCCATGGTTCTCAAGTGCTTCCAAGTGAAGCTCAATGAAGTGGCA
CACCTGGTACAGCCCCACCCCACAGATGCCTGGATGCTGATGCACTGGCTCCAGAGGGTAGGGAGCAGAGCAGCATGTCA
TCCACTTAGAACCCTAAAACAGTGCTACCCCCTTCCTGGAGGCATGCTTGCAGGCTGTGAGTGAAGGAACACTGCTGTAC
CTGACCTGAACCAACATGATGGTGCTGGCAGGAGCAGCTGAGAGACCTGCTATAGCAAGTCCATGGCCATGGCTCTCAAG
TGCTGGCCCTGCCACAAAATGTCCCTGAGGTTCATCCTGCATAACCTGAACCTCCAGGCCAGTATACTGCAGCCAGCACC
CCTGGTGCCACTGCTCATGTAAGGGACAACTTCTATCAATGTGCGTTTGTTGGAGTGTTCACCAGCAATGTCAATGTCAA
GCTCAAGGCCTGGGCATGCCAGCAGCACTGGTGTTCCAGTGCGTTGGTGTGGGCTTCTACCTTTAGTTCATCAGCAAGGC
AACAGAAGCCCCTGACAGTTGGCTCATGTTCTCTGCAGTCTGTGGTCCCTCTGTGACCCTGACCACTGAGTATGAGCATT
GTGGGCAGGAACACCAATTTGGAGGCCCCCTGTCAGAAGAGCCCCTCCACAAACTGGACTGTGTGGGCTGTGTCCTTGGG
GCTGTGAGCACCAGTTCCAGACACTTTGGCACCTCAGAGCAGGTATGTAGCATCCTTGGCATTGTTACTGGGGAACTCCC
AGATGATCCTCTCCACTACACACTGCATGGGCTAAACAGCACCCTCCTGTGTCAGCATGACCAGCCTCCTGCAGCTACAC
TCTGCCTTCCTCCACATGGGCTTCCCGTCTTGCTCTCACAAGCTGTAAGAACCTGGTCAGGATGGAGCCTCTGCCTTGTC
TCTCTGGAACCTTCTG
ORF - retro_ocun_1629 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 52.0 % |
| Parental protein coverage: | 91.51 % |
| Number of stop codons detected: | 7 |
| Number of frameshifts detected: | 10 |
Retrocopy - Parental Gene Alignment:
| Parental | RRLCRARFMEGHRQGPPSPAAMENGTEPRTEERPPEAQETTV-AEGAARIAFPSANEVFYNPVQEFNRDL |
| R.LCRA.FMEG..Q....PAAME.G......E..P.....T...EGA...A....N.VFY..V.EF..DL | |
| Retrocopy | RSLCRAWFMEGKPQASLNPAAMEKGKK-HCMEESPPEKK*TT>TEGAVTAASLTSN*VFYHRVEEFHGDL |
| Parental | TCAVITEFARL-QLGAKGIQIKVPGEKDVQKVVVDLSEREEEKTEPEDGENLAPGDQPRTAAVGEICEGG |
| ..AVITEFA....L..KG.QIKV...K....VVVDLSE..EE..E.....NL.PG.Q..TAA.G.ICEGG | |
| Retrocopy | M*AVITEFACI<HLESKGLQIKVSAGKNLKQVVVDLSEQDEEMAESKRYGNLGPGVQSSTAAAGVICEGG |
| Parental | LRVLEGLAASG-LRSIRFAREVPGLQSVLANDASARAVDLIRRNVQLNDVGHLVQPSQADARMLMYQHQK |
| L.VLEGL.ASG...SI...R.V...QSV..N..SA.A..L....V.LN.V.HLVQP...DA.MLM...Q. | |
| Retrocopy | LWVLEGLVASG<IQSIQLTRKVLEPQSVVTNNGSAKAMVLKCFQVKLNEVAHLVQPHPTDAWMLMHWLQR |
| Parental | VAERF-DVIDLDPYGSPASFLDAAVQAVSEGGLLCVTCTDMAVLAG-NSGETCYSKYGAMALKSRACHEM |
| V..R...VI.L.P..S...FL.A..QAVSEG.LL..T.T.M.VLAG..S.ETCYSK..AMALK...CH.M | |
| Retrocopy | VGSRA>HVIHLEP*NSATPFLEACLQAVSEGTLLYLT*TNMMVLAG<SS*ETCYSKSMAMALKCWPCHKM |
| Parental | ALRIVLHSLDLRANCYQRY-VVPLLS-LSADFYVRVFVRVFTGQA--KVKASASKQ-ALVFQCVGCGAFY |
| .LR..LH.L.L.A...Q....VPLL......FY...FV.VFT.....K.KA.A..Q.ALVFQCVG.G.FY | |
| Retrocopy | SLRFILHNLNLQASILQPAPLVPLLM<VRDNFYQCAFVGVFTSNVNVKLKAWACQQ<ALVFQCVGVG-FY |
| Parental | LQRLGKAAEAPGGRRVKFSAACGPPVA--PECEHCGQRHQLGGPLWAEPIHDLDFVGRVLEAVSANPSRF |
| L....KA.EAP......FSA.CGP.V....E.EHCGQ.HQ.GGPL..EP.H.LD.VG.VL.AVS.....F | |
| Retrocopy | L*FISKATEAPDSW-LMFSAVCGPSVTLTTEYEHCGQEHQFGGPLSEEPLHKLDCVGCVLGAVSTSSRHF |
| Parental | HTSERIRGVLSVVSEELPDVPLYYTLDQLSSTIRC-STPSLLQLRSALLHAGFRVSLSH-ACKNAVKTD- |
| .TSE.....L..V..ELPD.PL.YTL..L.ST..C.S..SLLQL.SA.LH.GF..S.SH..CKN.V.... | |
| Retrocopy | GTSEQVCSILGIVTGELPDDPLHYTLHGLNSTLLC>SMTSLLQLHSAFLHMGF-PSCSH>SCKNLVRME< |
| Parental | APASAVWDIM |
| A.A...W... | |
| Retrocopy | ASALSLWNLL |
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 | 10 .93 RPM |
| SRP017611_kidney | 0 .10 RPM | 12 .67 RPM |
| SRP017611_liver | 0 .00 RPM | 8 .63 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1629 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1629 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1629 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000104907 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000021934 | 1 retrocopy |
retro_ocun_1629 ,
|
| Pongo abelii | ENSPPYG00000009622 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000010557 | 1 retrocopy |