RetrogeneDB ID: | retro_xtro_51 | ||
Retrocopy location | Organism: | Xenopus (Xenopus tropicalis) | |
| Coordinates: | GL180723.1:3531..5103(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | mccc2 | ||
| Ensembl ID: | ENSXETG00000018213 | ||
| Aliases: | None | ||
| Description: | methylcrotonoyl-CoA carboxylase 2 (beta) [Source:Jamboree;Acc:XB-GENE-985830] |
Retrocopy-Parental alignment summary:
>retro_xtro_51
TCCACCGACTTCCAGGGCAATGCGGCCGCCATGCGCGCTCTGGTGCAGGAGTTGCGGGCCCATCTCGCCAAGGTCGCCCA
GGGTGGCGGCGAGGCCGCGCGTGCCAAGCACGTGGCGCGCGGCAAGATGCTGCCGCGCGAGCGCGTGCAGATGCTGCTTG
ACCCCGGCACGCCCTTTCTGGAACTGGCCCCGCTGGCGGCGCTGGATATGTACGGTAACGAGGCGCCGGGCGCGGGCATC
ATCGTCGGCCTGGGCCGCGTGAATGGCGTGGATTGCATGGTGGTGTGCAACGACGCCACGGTGAAGGGCGGCACCTACTA
CCCCATGACGGTGAAGAAGCACCTGCGCGCCCAGGAAGTGGCGGCGCAGAACCACCTGCCCTGCATCTACCTGGTCGATT
CGGGCGGCGCCAACCTGCCCAATCAGGACGACGTGTTTCCTGACCGCGAGCACTTCGGCCGCATCTTCTACAACCAGGCC
CACATGAGCGCCCAGGGCATCGCGCAGATCGCCGTGGTCATGGGCAGTTGCACGGCTGGCGGCGCCTACGTGCCGGCGAT
GAGCGACGAATCCATCATCGTCAAGAACCAGGGCACTATCTTTCTGGGTGGCCCGCCGCTGGTGAAGGCCGCCACGGGCG
AGGTGGTGAGCGCCGAAGACCTGGGCGGCGGCGACGTGCACACGCGCCTCTCGGGCGTGGCCGACCATCTGGCGCAGAAC
GATATGCACGCGCTGGCGCTGGCGCGCGCGGCTGTGGCCAATTTGAATAGAAACAAGCCGCAAAACCCCGCCGATCAAGC
GCCAGCTGCTCCTCAATATGAAGCACAGGAACTGTATGGCGTGATCCCTACCGACACGCGCAAGCCCTTCGACGTGCGCG
AGATCATCGCGCGCATCGTCGATGGCAGCGCGTTCGACGAATTCAAGGCGCGCTTCGGCGCCACTCTGGTGTGCGGCTTT
GCGCGCATCGAGGGCATGCAGGTTGGCGTCATCGCCAACAACGGTATTTTGTTCAGCGAAAGCGCGCAAAAGGGCGCGCA
CTTCATCGCGTTGTGCTGCCAGCGCAAGGTTCCGCTGGTGTTTCTGCAGAACATCACCGGCTTCATGGTCGGGCGCAAGT
ACGAGAACGAGGGCATCGCACGCCACGGCGCCAAGCTGGTCACGGCCGTGGCCACGGCGCGTGTGCCCAAGTTCACCATC
ATCATTGGCGGCAGCTTTGGCGCTGGCAACTACGGCATGTGTGGCCGCGCCTACAGCCCGCGCTTCCTCTGGATGTGGCC
CAACGCGCGCATTTCCGTGATGGGCGGTGAGCAGGCCGCCAGCGTGCTGGCCACCGTCAAGCGCGACGGCATCGAGGCCC
AGGGCGGCAGCTGGAGCGCCGAGGAGGAGGAAGCCTTCAAGGCCCCCATCCGCCGCCAGTACGAGGAACAGGGCCACCCC
TACTACGCCACCGCGCGCCTGTGGGACGACGGCGTGATCGACCCCGCCGACACGCGCCGCGTGCTCGCGCTGGGCCTCTC
GGCCACGCGCAACGCGCCCATCGAGGACACCCGGTTTGGCGTGTTCCGCATG
ORF - retro_xtro_51 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 65.97 % |
| Parental protein coverage: | 92.93 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | SPAYQESYDRMKALVTELKERAQKIRLEGCGYPLNAYHTAVGRFLDREKVHLKINHISAFLEFSQFAGYQ |
| S...Q.....M.ALV.EL.....K....G.G....A.H.A.G..L.RE.V.........FLE....A... | |
| Retrocopy | STDFQGNAAAMRALVQELRAHLAKVA-QGGGEAARAKHVARGKMLPRERVQMLLDPGTPFLELAPLAALD |
| Parental | LYGNEEVPAGGIISGIGRVSGVECLIVANDATVKGGSYYPITVKKHLRAQEIAMQNNLPCVYLVDSGGAN |
| .YGNE..P..GII.G.GRV.GV.C..V.NDATVKGG.YYP.TVKKHLRAQE.A.QN.LPC.YLVDSGGAN | |
| Retrocopy | MYGNE-APGAGIIVGLGRVNGVDCMVVCNDATVKGGTYYPMTVKKHLRAQEVAAQNHLPCIYLVDSGGAN |
| Parental | LPRQAEVFPDRDHFGRIFYNQARMSSQGISQIAVVMGSCTAGGAYVPAMADESIIVRKQGTIFLGGPPLV |
| LP.Q..VFPDR.HFGRIFYNQA.MS.QGI.QIAVVMGSCTAGGAYVPAM.DESIIV..QGTIFLGGPPLV | |
| Retrocopy | LPNQDDVFPDREHFGRIFYNQAHMSAQGIAQIAVVMGSCTAGGAYVPAMSDESIIVKNQGTIFLGGPPLV |
| Parental | KAATGEEVSAEDLGGADLHCRKSGVTDHYALDDNHALHLARKAVRSLNYNKNLDVTVEKPEDPVFPADEL |
| KAATGE.VSAEDLGG.D.H.R.SGV.DH.A..D.HAL.LAR.AV..LN.NK........P..P...A.EL | |
| Retrocopy | KAATGEVVSAEDLGGGDVHTRLSGVADHLAQNDMHALALARAAVANLNRNKPQNPADQAPAAPQYEAQEL |
| Parental | YGIVGANLKKNVDVREVIARVVDGSKFDEFKALYGDTLITGFARIYGYPVGIIGNNGVLFSESAKKGTHF |
| YG.......K..DVRE.IAR.VDGS.FDEFKA..G.TL..GFARI.G..VG.I.NNG.LFSESA.KG.HF | |
| Retrocopy | YGVIPTDTRKPFDVREIIARIVDGSAFDEFKARFGATLVCGFARIEGMQVGVIANNGILFSESAQKGAHF |
| Parental | IQLCCQRNIPLIFLQNITGFMVGRDYEAGGIAKDGAKMVTAVACANVPKITVIIGGSYGAGNYGMCGRAY |
| I.LCCQR..PL.FLQNITGFMVGR.YE..GIA..GAK.VTAVA.A.VPK.T.IIGGS.GAGNYGMCGRAY | |
| Retrocopy | IALCCQRKVPLVFLQNITGFMVGRKYENEGIARHGAKLVTAVATARVPKFTIIIGGSFGAGNYGMCGRAY |
| Parental | SPRFLYMWPNARISVMGGEQAATVLATIAKDQKAREGKQFSEQEEAALKEPIIRRFEEEGNPYYSSARLW |
| SPRFL.MWPNARISVMGGEQAA.VLAT...D.....G...S..EE.A.K.PI.R..EE.G.PYY..ARLW | |
| Retrocopy | SPRFLWMWPNARISVMGGEQAASVLATVKRDGIEAQGGSWSAEEEEAFKAPIRRQYEEQGHPYYATARLW |
| Parental | DDGIIDPADTRLVLGLSLSAALNAPTQKTQFGVFRM |
| DDG.IDPADTR.VL.L.LSA..NAP...T.FGVFRM | |
| Retrocopy | DDGVIDPADTRRVLALGLSATRNAPIEDTRFGVFRM |
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 | 16 .75 RPM |
| SRP007412_heart | 0 .00 RPM | 24 .43 RPM |
| SRP007412_kidney | 0 .00 RPM | 24 .43 RPM |
| SRP007412_liver | 0 .00 RPM | 7 .79 RPM |
| SRP007412_skeletal_muscle | 0 .00 RPM | 13 .38 RPM |
Xenopus tropicalis was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_xtro_51 retrocopy.
Xenopus tropicalis was not studied using FANTOM5 data.
retro_xtro_51 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 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Xenopus tropicalis | ENSXETG00000018213 | 1 retrocopy |
retro_xtro_51 ,
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