RetrogeneDB ID: | retro_xtro_69 | ||
Retrocopy location | Organism: | Xenopus (Xenopus tropicalis) | |
| Coordinates: | GL187592.1:2183..2942(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | nubpl | ||
| Ensembl ID: | ENSXETG00000014129 | ||
| Aliases: | None | ||
| Description: | nucleotide binding protein-like [Source:Jamboree;Acc:XB-GENE-971259] |
Retrocopy-Parental alignment summary:
>retro_xtro_69
CCGTTGCCGGGGGTGAAAAACATCATCGCCGTGGCCTCGGGCAAGGGCGGTGTGGGCAAGAGCACCACGGCTGTCAATCT
GGCCCTGGCGCTGGTGGCCGAGGGCGCGCGCGTGGGCCTGCTGGATGCCGATATCTACGGCCCCAGCCAGCCCATGATGA
CCGGCACTTCGGGCGAATTGGAAAGCCTGGATGGCAAGCTGATGGAGCCCAAGCGCGCCATGGGGCTGCAAATCAATTCC
ATCGGCTTCCTCGTCAAGGACGAACAGGCCATGATCTGGCGCGGCCCCATGGCCAGTCAGGCGCTGGAGCAACTCGTTAC
GCAGACGCGCTGGGACGATCTGGACTACCTGCTGGTGGATATGCCCCCCGGCACCGGCGACATCCAGCTCACCATGGCGC
AGAAGGTGCCGCTGACTGGCGCGATCATCGTCACTACGCCGCAGGATATTGCGCTGCTCGACGCCAGGAAGGGCATCACC
ATGTTCCAGAAGGTGAACGTGCCCATCCTCGGCATCGTCGAGAACATGGCTGTGCACGTGTGCAGCCACTGCGGCCATGT
GGAGCACATTTTCGGCCAGGACGGTGGCAAGAAGATGGCGCAAAGCCAGGGCATGGACTACCTGGGCGCGCTGCCGCTGC
GCCTGTCGATCCGCGAGCAGGCCGACAGTGGCTGCCCCACCGTGGCCGCCGAGCCCGACGGCGACGTGGCGCGCATCTAC
AAAACCATCGCCCGCGCGGTGGCGGTGAAGATCGCGCAG
ORF - retro_xtro_69 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 51.76 % |
| Parental protein coverage: | 79.94 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | PIPGVKHVVVVASGKGGVGKSTTAVNLALGIAASDQVKAVGLLDADVYGPSIPRMMNLKGNPEVSNKNLM |
| P.PGVK....VASGKGGVGKSTTAVNLAL...A......VGLLDAD.YGPS.P.M....G..E.....LM | |
| Retrocopy | PLPGVKNIIAVASGKGGVGKSTTAVNLALALVAEGA--RVGLLDADIYGPSQPMMTGTSGELESLDGKLM |
| Parental | IPLFNYGIRCMSMGFLVEETAPIVWRGLMVMSAIEKLLRQVEWGELDYLVIDMPPGTGDVQLSISQNIPI |
| .P....G....S.GFLV.......WRG.M...A.E.L..Q..W..LDYL..DMPPGTGD.QL...Q..P. | |
| Retrocopy | EPKRAMGLQINSIGFLVKDEQAMIWRGPMASQALEQLVTQTRWDDLDYLLVDMPPGTGDIQLTMAQKVPL |
| Parental | SGAVIVSTPQDIALVDARRGAEMFQKVNVPVLGFVQNMSIFQCPKCNHETHIFGEEGARRLAESLGFDIL |
| .GA.IV.TPQDIAL.DAR.G..MFQKVNVP.LG.V.NM....C..C.H..HIFG..G....A.S.G.D.L | |
| Retrocopy | TGAIIVTTPQDIALLDARKGITMFQKVNVPILGIVENMAVHVCSHCGHVEHIFGQDGGKKMAQSQGMDYL |
| Parental | GDIPLHINIRETSDQGRPVVVSDPQSSEAKAYLKIASEVLRRISK |
| G..PL...IRE..D.G.P.V...P....A..Y..IA..V...I.. | |
| Retrocopy | GALPLRLSIREQADSGCPTVAAEPDGDVARIYKTIARAVAVKIAQ |
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 | 15 .85 RPM |
| SRP007412_heart | 0 .00 RPM | 10 .89 RPM |
| SRP007412_kidney | 0 .00 RPM | 10 .89 RPM |
| SRP007412_liver | 0 .00 RPM | 9 .12 RPM |
| SRP007412_skeletal_muscle | 0 .00 RPM | 8 .38 RPM |
Xenopus tropicalis was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_xtro_69 retrocopy.
Xenopus tropicalis was not studied using FANTOM5 data.
retro_xtro_69 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 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000035142 | 1 retrocopy | |
| Xenopus tropicalis | ENSXETG00000014129 | 1 retrocopy |
retro_xtro_69 ,
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