RetrogeneDB ID: | retro_ocun_1952 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | X:109275027..109275684(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TTLL1 | ||
| Ensembl ID: | ENSOCUG00000016224 | ||
| Aliases: | None | ||
| Description: | tubulin tyrosine ligase-like family, member 1 [Source:HGNC Symbol;Acc:1312] |
Retrocopy-Parental alignment summary:
>retro_ocun_1952
AGAAGGGTATCTTCCATCAACAAGCTCTCTGACATCATGAAGTGGCCGGGGACAGCAAGATGTCCTCGCTTGTGTCCCAA
CCTACCAAGGAAACCTACATGATCTCCCTGTACATTAACAACCTGTTGCTCAACAGGGCAAGGAAATTTGACCTGTGCCA
TCCCTTCTGGTGTTCACGTACCACCACTGCACTAGTACATGTACAAGCTTGGCTTCTGCCGATTCTGCATGGTGTACACC
CCAAGGACCAGTGAGCTACACAACATGTTCCTGCATTGCACCAGTGTGGCTATTCAGAAGGACTACAACCACATTCACTG
GGCAAGGGGGCTGTGAGCAATCTGCATCTGTACCTGGTAAGTACCCACGACAGGGAGGTGACCAGCAAGCTGTCTGACAA
GGTCCACTGCACCATTGTGCAGTCCCTGAAGACTGTGGTGCCAGTGGTGAGCAATGACAAGCACTGCTTTGAGTGCTATG
GCTATGACATCATCGTCAACGATGAGCTGAAGCCCTGGCCGATGAGGTTAACACATCCCCATCTCTTACTTCCAGCACCA
CCAACGGCCAGATCCTTAAGTACAACCTGATTCATGACACTCACATATTGTGGTCCCCAGTGGTAAAATCCCAGATTTCA
GATGGAACAAGCCTCCC
ORF - retro_ocun_1952 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.94 % |
| Parental protein coverage: | 53.19 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | RGIFLINKLSQIKKW-SRDSKTSSFVSQSTKEAYVISLYINN-PLLIGGRKFDLRLYVLVSTYR-PLRCY |
| R....INKLS.I.KW...DSK.SS.VSQ.TKE.Y.ISLYINN.P....G.........LV.TY..PL..Y | |
| Retrocopy | RRVSSINKLSDIMKW<AGDSKMSSLVSQPTKETYMISLYINN<PVAQQGKEI*PVPSLLVFTYH<PLH*Y |
| Parental | MYKLGFCRFCTVRYTPSTSELDNMFVHLTNVAIQKHGEDYNHIHG-GKWTVSNLRLYLESTRGREVTSKL |
| MYKLGFCRFC.V.YTP.TSEL.NMF.H.T.VAIQK...DYNHIH..GK..VSNL.LYL.ST..REVTSKL | |
| Retrocopy | MYKLGFCRFCMV-YTPRTSELHNMFLHCTSVAIQK---DYNHIHW<GKGAVSNLHLYLVSTHDREVTSKL |
| Parental | FDEIHWIIVQSLKAVAPVMNNDKHCFECYGYDIIIDDKLKPWLI-EVNASPSLTSSTANDRILKYNLIND |
| .D..H..IVQSLK.V.PV..NDKHCFECYGYDII..D.LKPW...EVN.SPSLTSST.N..ILKYNLI.D | |
| Retrocopy | SDKVHCTIVQSLKTVVPVVSNDKHCFECYGYDIIVNDELKPWPM<EVNTSPSLTSSTTNGQILKYNLIHD |
| Parental | T-LNIAVPNGEVPDCKWNKSP |
| T...I.VP.G..PD..WNK.P | |
| Retrocopy | T<SHIVVPSGKIPDFRWNKPP |
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 | 44 .32 RPM |
| SRP017611_kidney | 0 .00 RPM | 23 .01 RPM |
| SRP017611_liver | 0 .00 RPM | 8 .32 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1952 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1952 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1952 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 | |
|---|---|---|---|
| Erinaceus europaeus | ENSEEUG00000004854 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000016224 | 1 retrocopy |
retro_ocun_1952 ,
|
| Drosophila melanogaster | FBgn0030823 | 1 retrocopy |