RetrogeneDB ID: | retro_xtro_54 | ||
Retrocopy location | Organism: | Xenopus (Xenopus tropicalis) | |
| Coordinates: | GL181088.1:2800..3550(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | etfb | ||
| Ensembl ID: | ENSXETG00000022222 | ||
| Aliases: | None | ||
| Description: | electron-transfer-flavoprotein, beta polypeptide [Source:Jamboree;Acc:XB-GENE-956098] |
Retrocopy-Parental alignment summary:
>retro_xtro_54
ATGAAGATGAAAGTTCTGATCTCCGTAAAACGCGTAGTGGACTACAACGTGAAGGTTCGCGTGAAATCGGACAGCACGGG
CGTAGACATCGCCAACGTCAAGATGAGCATGAACCCCTTCGACGAAATCGCCGTCGAGGAGGCCGTGCGCCTCAAAGAAA
AGGGTGTGGCCACCGAGGTCATCGCCGTGAGCTGTGGCGTGGCGCAATGCCAGGAGACGCTACGCACCGCCATGGCCATA
GGCGCCGACCGCGCGGTTCTTGTGGAAACCGACGCCGAACTACAGCCCCTGGCCGTGGCCAAACTCCTGAAGGCCCTGAT
GAACAAGGAACAGCCCGACCTCATCATCCTGGGCAAACAGGCCATCGACGACGACGCCAACCAGACCGGCCAGATGCTCG
CCGCGCTGGCCGATCTGCCGCAAGCCACGTTCGCTTCCAAGGTGGAACTGAGTGCCGACGCCGCGACCGTGACGCGCGAG
GTCGACGGCGGCCTGGAGACGCTGCAATTGACCCTGCCAGCCGTGATTACCACCGACCTGCGCCTGAACGAGCCGCGCTA
CGTCACGCTGCCCAACATCATGAAGGCCAAGAAGAAGACGCTGGATACCGTCAGGCCCGCCGATTTGGGCGTGGACGTGG
CTCCGCGCCTCAAGACCCTCAAGGTGAGCGAGCCCGCCAAGCGCGGCGCTGGCGTCAAGGTGCCCGATGTGGCCGCCCTG
GTTGAGAAACTCAAGAACGAAGCCAAGGTC
ORF - retro_xtro_54 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 61.81 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MALRALVGVKRVIDYAVKVRVKPDKTGVVTDGVKHSMNPFCEIAVEEAVRLKEKKIVSEIIAVSCGPQQC |
| M....L..VKRV.DY.VKVRVK.D.TGV....VK.SMNPF.EIAVEEAVRLKEK....E.IAVSCG..QC | |
| Retrocopy | MKMKVLISVKRVVDYNVKVRVKSDSTGVDIANVKMSMNPFDEIAVEEAVRLKEKGVATEVIAVSCGVAQC |
| Parental | QETIRTALAMGADRGIHVEVAAKDAESLGPFQVSKIMAALAKKENVNLVLMGKQAIDDDCNQTGQMTAAL |
| QET.RTA.A.GADR...VE....DAE.L.P..V.K...AL..KE...L...GKQAIDDD.NQTGQM.AAL | |
| Retrocopy | QETLRTAMAIGADRAVLVET---DAE-LQPLAVAKLLKALMNKEQPDLIILGKQAIDDDANQTGQMLAAL |
| Parental | LDWPQGTFASEVKVEGEKLTVVREVDGGLETISVKLPAVVTADLRLNEPRYATLPNIMKAKKKKIETVKP |
| .D.PQ.TFAS.V.......TV.REVDGGLET....LPAV.T.DLRLNEPRY.TLPNIMKAKKK...TV.P | |
| Retrocopy | ADLPQATFASKVELSADAATVTREVDGGLETLQLTLPAVITTDLRLNEPRYVTLPNIMKAKKKTLDTVRP |
| Parental | SDLGVDITSRIRVLSVEDPPQRLAGVKVETVQDLVSKLKESGRI |
| .DLGVD...R...L.V..P..R.AGVKV..V..LV.KLK..... | |
| Retrocopy | ADLGVDVAPRLKTLKVSEPAKRGAGVKVPDVAALVEKLKNEAKV |
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 | 12 .46 RPM |
| SRP007412_heart | 0 .00 RPM | 87 .03 RPM |
| SRP007412_kidney | 0 .00 RPM | 87 .03 RPM |
| SRP007412_liver | 0 .00 RPM | 26 .10 RPM |
| SRP007412_skeletal_muscle | 0 .00 RPM | 50 .86 RPM |
Xenopus tropicalis was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_xtro_54 retrocopy.
Xenopus tropicalis was not studied using FANTOM5 data.
retro_xtro_54 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 | |
|---|---|---|---|
| Ailuropoda melanoleuca | ENSAMEG00000014360 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000003974 | 1 retrocopy | |
| Xenopus tropicalis | ENSXETG00000022222 | 1 retrocopy |
retro_xtro_54 ,
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