RetrogeneDB ID: | retro_xtro_34 | ||
Retrocopy location | Organism: | Xenopus (Xenopus tropicalis) | |
| Coordinates: | GL174257.1:34190..34931(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | enosf1 | ||
| Ensembl ID: | ENSXETG00000003158 | ||
| Aliases: | None | ||
| Description: | enolase superfamily member 1 [Source:Jamboree;Acc:XB-GENE-940740] |
Retrocopy-Parental alignment summary:
>retro_xtro_34
ACCATTACCGCGATTCGCGTCGAAGATATCCGCTTTCCTACGTCCCAGTCCCTGGACGGTTCCGACGCCATGAACCCGGA
CCCGGACTACTCGGCCGCCTATGTGATTTTGCAGACCGACAACCCGGCCCTTGAAGGCCATGGCCTGACCTTCACCATCG
GCCGTGGCAACGAGATTTGCTGTGCGGCGATCCAGGCCATGCAGCCGCTGTTGATAGGCTTGACCCTGGAATGGATCGCC
GAAGACATGGGCCGTTTCTGGCGGCATATCACCAGCGACAGCCAGTTGCGCTGGATTGGCCCGGACAAGGGCGCCATTCA
CCTGGCCACCGGCGCGATCGTCAACGCCGCGTGGGATTTGTGGGCCAAGGCCGAAGGAAAACCCTTGTGGCGCCTGGTGG
CCGACATGAGTCCGGAACAGTTGGTGCGGTGCATCGACTTCCGCTACATCACCGACTGCATCACCTCCAGCGAAGCCCTG
GCCTTGCTGCGCCAACGCGCCGAAGGCAAGGCTGAACGCATGGCCGACCTGCAAGCCAATGGCTACCCCTGCTACACCAC
CTCGGCCGGCTGGCTCGGTTATGGCGACGAAAAGCTGCGCAGGCTGTGCCAGGAAGCGGTGGATGCAGGCTTCAACCACG
TCAAGCTCAAGGTCGGCCATGACTTGCAGGACGACCTGCGCCGCGTGCGCATCGCCCGCGAAGTGCTGGGGCCGGACCGC
CAACTGATGATCGACGCCAAC
ORF - retro_xtro_34 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 54.03 % |
| Parental protein coverage: | 55.98 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | TITSLHVTDVRFPTSLDQHGSDAMHTDPDYSAAYIVIETDAADGLKGHGLTFTLGKGTEIVVCAVRALSR |
| TIT...V.D.RFPTS....GSDAM..DPDYSAAY....TD....L.GHGLTFT.G.G.EI...A..A... | |
| Retrocopy | TITAIRVEDIRFPTSQSLDGSDAMNPDPDYSAAYVILQTDNP-ALEGHGLTFTIGRGNEICCAAIQAMQP |
| Parental | HVIGKALGDIVNNFRDFYRQLTSDGQLRWIGPEKGAVQLATAAVLNAVWDLWAKKEKKPLWKLLVDMDPH |
| ..IG..L..I......F.R..TSD.QLRWIGP.KGA..LAT.A..NA.WDLWAK.E.KPLW.L..DM.P. | |
| Retrocopy | LLIGLTLEWIAEDMGRFWRHITSDSQLRWIGPDKGAIHLATGAIVNAAWDLWAKAEGKPLWRLVADMSPE |
| Parental | QLVSCIDFRYITDALTEEEALEILQNGKQGQRDREEHMLRSGYPAYTTSCAWLGYSDEQLKKLCSDALKE |
| QLV.CIDFRYITD..T..EAL..L.....G...R.......GYP.YTTS..WLGY.DE.L..LC..A... | |
| Retrocopy | QLVRCIDFRYITDCITSSEALALLRQRAEGKAERMADLQANGYPCYTTSAGWLGYGDEKLRRLCQEAVDA |
| Parental | GWTRFKVKVGADLKDDIRRCELIRGMIGPDNIMMLDAN |
| G....K.KVG.DL.DD.RR....R...GPD...M.DAN | |
| Retrocopy | GFNHVKLKVGHDLQDDLRRVRIAREVLGPDRQLMIDAN |
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 | 2 .98 RPM |
| SRP007412_heart | 0 .00 RPM | 9 .56 RPM |
| SRP007412_kidney | 0 .00 RPM | 9 .56 RPM |
| SRP007412_liver | 0 .00 RPM | 16 .07 RPM |
| SRP007412_skeletal_muscle | 0 .00 RPM | 4 .07 RPM |
Xenopus tropicalis was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_xtro_34 retrocopy.
Xenopus tropicalis was not studied using FANTOM5 data.
retro_xtro_34 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 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Xenopus tropicalis | ENSXETG00000003158 | 3 retrocopies |
retro_xtro_34 , retro_xtro_36, retro_xtro_44,
|