RetrogeneDB ID: | retro_xtro_56 | ||
Retrocopy location | Organism: | Xenopus (Xenopus tropicalis) | |
| Coordinates: | GL181419.1:1..1399(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | aldh6a1 | ||
| Ensembl ID: | ENSXETG00000013304 | ||
| Aliases: | None | ||
| Description: | aldehyde dehydrogenase 6 family, member A1 [Source:Jamboree;Acc:XB-GENE-1006692] |
Retrocopy-Parental alignment summary:
>retro_xtro_56
TGGCGCGATGTGACCAATCCCGCCACGCAGGAAGTCGTCGCCCGCGTGCCCTTCGCCACGCGCGACGAGGTGAACCTTGC
CGTCGCCAACGCGCAGCAAGCCTTCCAGACCTGGCGCGAGACGTCGCTGGCCGCGCGCATGCGCATCATGCTGAAGCTGC
AGCAGCTGCTGCGCGAGCACACGGCCGAGTTGGCCCAGCTCATCACGCGCGAGCACGGCAAGACCCTGCCCGACGCCGAG
GGCGAAGTGGCGCGCGGCCTGGAAGTGGTGGAGCACGCCTGCTCCATCACCACGTTGCAGCTCGGCGAGATGGCCGAGAA
TGCCGCCACTGGCGTTGACGTGTACAACCTGCTGCAACCCCTGGGCGTGGGTGCGGGCATCACGGCCTTCAACTTCCCGG
TGATGCTGCCGTGCTTCATGTTTCCCATGGCCATCGCCTGCGGCAATACTTTCGTGCTCAAGCCGTCGGAGCAGGATCCC
AGTTCCACCATGCGTCTGGTGGAACTGGCGCACGAGGCTGGCGTGCCGCCCGGTGTGCTCAATGTGATCCACGGCGGGCC
GGAAGTGGCCGACGTGCTGTGCGACCACCCCGACATCAAGGCGCTGTCATTCATCGGCTCCACCCACGTTGGCACGCACG
TCTACCGCCGCGCCAGCGAGGCGGGCAAGCGCGTGCAGTCGATGATGGGCGCCAAAAACCACTGCGTGGTGATGCCCGAC
GCGCCCAAGGAACACGCGTTGAACAACCTGCTCGGCTCGGCCTTCGGCGCCGCTGGCCAGCGCTGCATGGCCAACTCGGT
GGCGGTGCTCGTGGGCGCGGCGCGCGACTGGCTGCCCGAACTGGTGGAAAAGTCCAAGGCCATGAAGGTTGGCCCCGGCA
GTGACCGCGATGCCGACCTGGGCCCGCTGGTCAACCCGCGCGCCAGGCAGCGCGTGCTGGATCTGATCGACACCGGTGTG
GCCCAAGGCGCCAGACTGCTGCTGGACGGGCGCGGCTGCGTGGTGCCCGGCTATGAAAAGGGCAACTTCGTCGGCCCCAC
GGTGTTCGCCGACGTGACTGAAGCCATGGACATCTACCAGCAGGAGATCTTCGGCCCCGTGCTCAACGTGGTGTGCGTGG
ACACGCTGGAAGACGCCATCGCCTTCATCAACCGCAACCCCAACGGCAACGGCACCTCCATTTTCACCAGCAGCGGCTGG
GCGGCGCGCAGGTTCCAGCACGACATCAACGTCGGCCAGGTGGGCATCAACGTGCCGATCCCCGTGCCCGTGGCCTACTT
CAGCTTCACTGGTTCGCGCGCCTCCAAACTCGGCGACCTGGGCCCCAACGGCAAGCAGGCCGTGCAGTTCTGGACTCAGA
CCAAGACCGTCACCGCCCGCTGGTACGAGGAAGGCAGC
ORF - retro_xtro_56 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 57.3 % |
| Parental protein coverage: | 89.1 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | WIDVHNPATNEVIGRVPQATQSEMEAAVNACQRTFPAWSETSILNRQQIFLRYQQLIKDNLKEVARLITL |
| W.DV.NPAT.EV..RVP.AT..E...AV...Q..F..W.ETS...R..I.L..QQL......E.A.LIT. | |
| Retrocopy | WRDVTNPATQEVVARVPFATRDEVNLAVANAQQAFQTWRETSLAARMRIMLKLQQLLREHTAELAQLITR |
| Parental | EQGKTLADAEGDVFRGLQVVEHACSVTSLMLGETLSSLTKDMDTFTFRLPLGVCAGIAPFNFPAMIPLWM |
| E.GKTL.DAEG.V.RGL.VVEHACS.T.L.LGE.........D......PLGV.AGI..FNFP.M.P..M | |
| Retrocopy | EHGKTLPDAEGEVARGLEVVEHACSITTLQLGEMAENAATGVDVYNLLQPLGVGAGITAFNFPVMLPCFM |
| Parental | FPMAMVCGNTYLMKPSERVPGATMFLVQLLQDAGVPDGTINIIHGQHAAVNFICDHPAIRAISFVGSNQA |
| FPMA..CGNT...KPSE..P..TM.LV.L...AGVP.G..N.IHG........CDHP.I.A.SF.GS... | |
| Retrocopy | FPMAIACGNTFVLKPSEQDPSSTMRLVELAHEAGVPPGVLNVIHGGPEVADVLCDHPDIKALSFIGSTHV |
| Parental | GEYIYDRGSRNGKRVQSNMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEAKQWLPE |
| G...Y.R.S..GKRVQS.MGAKNH.VVMPDA.KE..LN.L.G.AFGAAGQRCMA.S.AVLVG.A..WLPE | |
| Retrocopy | GTHVYRRASEAGKRVQSMMGAKNHCVVMPDAPKEHALNNLLGSAFGAAGQRCMANSVAVLVGAARDWLPE |
| Parental | LVEKAKKLQVNAGDQPGADLGPLISPAAKDRVCSLVESGVREGATLLLDGRDVNVKGFENGNFVGPTILA |
| LVEK.K...V..G....ADLGPL..P.A..RV..L...GV..GA.LLLDGR...V.G.E.GNFVGPT..A | |
| Retrocopy | LVEKSKAMKVGPGSDRDADLGPLVNPRARQRVLDLIDTGVAQGARLLLDGRGCVVPGYEKGNFVGPTVFA |
| Parental | NVQPHMTCYKEEIFGPVLVILEADTLDDALKIVNSNPYGNGTAIFTTNGATARKYTHLVDVGQVGVNVPI |
| .V...M..Y..EIFGPVL.....DTL.DA....N.NP.GNGT.IFT..G..AR...H...VGQVG.NVPI | |
| Retrocopy | DVTEAMDIYQQEIFGPVLNVVCVDTLEDAIAFINRNPNGNGTSIFTSSGWAARRFQHDINVGQVGINVPI |
| Parental | PVPLPMFSFTGSRASFRGDTNFYGKQGVHFYTQLKTVTSQWKEEDS |
| PVP...FSFTGSRAS..GD....GKQ.V.F.TQ.KTVT..W.EE.S | |
| Retrocopy | PVPVAYFSFTGSRASKLGDLGPNGKQAVQFWTQTKTVTARWYEEGS |
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 |
|---|---|---|
| SRP007412_brain | 0 .00 RPM | 46 .87 RPM |
| SRP007412_heart | 0 .00 RPM | 162 .80 RPM |
| SRP007412_kidney | 0 .00 RPM | 162 .80 RPM |
| SRP007412_liver | 0 .00 RPM | 91 .67 RPM |
| SRP007412_skeletal_muscle | 0 .00 RPM | 63 .56 RPM |
Xenopus tropicalis was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_xtro_56 retrocopy.
Xenopus tropicalis was not studied using FANTOM5 data.
retro_xtro_56 was not experimentally validated.
Retrocopy orthology:
Xenopus tropicalis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000002670 | 1 retrocopy | |
| Xenopus tropicalis | ENSXETG00000013304 | 1 retrocopy |
retro_xtro_56 ,
|
| Xenopus tropicalis | ENSXETG00000020930 | 1 retrocopy |