RetrogeneDB ID: | retro_xtro_59 | ||
Retrocopy location | Organism: | Xenopus (Xenopus tropicalis) | |
| Coordinates: | GL181791.1:12310..13111(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | agmat | ||
| Ensembl ID: | ENSXETG00000025999 | ||
| Aliases: | None | ||
| Description: | agmatine ureohydrolase (agmatinase) [Source:Jamboree;Acc:XB-GENE-997016] |
Retrocopy-Parental alignment summary:
>retro_xtro_59
GACCTGGGCACATCCAACCGCACCGGAGCACGTTTCGGCCCACGGGCCATCCGGGCCGAATCCGTGCTGCTGCGCCCCTA
CAACATGGCCACCCGTGCCGCGCCGTTCGACTCGCTGCAAGTCGCAGACCTGGGCGATGTGGCCATCAATCCGTACAACC
TGGCCGACTCGATTGCGCGGATCGAAGGGGCGTACGACCAGATCGTGTCCAGCGGCTGCCGCCCCATCACACTCGGTGGA
GATCACACGGTGACGCTGCCGGTGCTTCGTGCGATGAAGCGTCGCTATGGTTCGCTGGCCTTGATTCATGTGGACGCGCA
CGCCGACGTGAACGACACCATGTTCGGTGAAAAGATCGCCCACGGTACACCGTTCCGGCGGGCGGTCGAGGAAGGCCTGT
TGCTCACCAGCCGGGTGACCCAGATCGGACTGCGTGGCACCGGTTATTCAGCAGAGGATTTCGACTGGTGCCGCGATCAG
GGCTTTACCGTCGTGCAGGTCGAACAGGTGTGGAGACGGTCGCTCGAACCGCTGATGGATGCGGTGAGAACCCGCGTGGG
TGAAGCGCCGGTGTACCTGAGTTTCGACATCGACGGCATCGACCCGGCGTTCGCACCGGGCACCGGCACGCCCGAAATTG
CAGGACTGACGGTGCCGCAGGCGCTGGAGATCATCCGGGGCTGCCGGGGCCTGAACCTGGTGGGTGCCGATCTGGTCGAG
GTGTCACCACCCTACGACGCTGCTGGTACCACCGCGCTACTGGGCGCCAACCTTGCCTACGAGATGCTCTGTGTGATGCC
G
ORF - retro_xtro_59 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.42 % |
| Parental protein coverage: | 78.3 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | DTGTSNRPGARFGPRHIRGESCMVRRYNISTRAAPFESLMVADIGDVNVNLYDLKDSCRRIRETYQKIMA |
| D.GTSNR.GARFGPR.IR.ES...R.YN..TRAAPF.SL.VAD.GDV..N.Y.L.DS..RI...Y..I.. | |
| Retrocopy | DLGTSNRTGARFGPRAIRAESVLLRPYNMATRAAPFDSLQVADLGDVAINPYNLADSIARIEGAYDQIVS |
| Parental | AGCIPLTLGGDHTITYPILQAVAEKHGPVGLVHVDAHTDTGDTALGEKIYHGTPFRRCVDEGLLDCKRVV |
| .GC.P.TLGGDHT.T.P.L.A.....G...L.HVDAH.D..DT..GEKI.HGTPFRR.V.EGLL...RV. | |
| Retrocopy | SGCRPITLGGDHTVTLPVLRAMKRRYGSLALIHVDAHADVNDTMFGEKIAHGTPFRRAVEEGLLLTSRVT |
| Parental | QIGIRGSSYSADPYGFCREQGFRVVLAEDCWFRSLVPLMAEVRSQMGAGPVYISFDIDGLDPSFAPGTGT |
| QIG.RG..YSA.....CR.QGF.VV..E..W.RSL.PLM..VR...G..PVY.SFDIDG.DP.FAPGTGT | |
| Retrocopy | QIGLRGTGYSAEDFDWCRDQGFTVVQVEQVWRRSLEPLMDAVRTRVGEAPVYLSFDIDGIDPAFAPGTGT |
| Parental | PEIAGLTTSQGLEIIRGCRGLNVVGCDLVEVAPVYDQSGNTALTGANLLFEMLCVLP |
| PEIAGLT..Q.LEIIRGCRGLN.VG.DLVEV.P.YD..G.TAL.GANL..EMLCV.P | |
| Retrocopy | PEIAGLTVPQALEIIRGCRGLNLVGADLVEVSPPYDAAGTTALLGANLAYEMLCVMP |
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 .56 RPM |
| SRP007412_heart | 0 .00 RPM | 1 .71 RPM |
| SRP007412_kidney | 0 .00 RPM | 1 .71 RPM |
| SRP007412_liver | 0 .00 RPM | 25 .97 RPM |
| SRP007412_skeletal_muscle | 0 .00 RPM | 12 .70 RPM |
Xenopus tropicalis was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_xtro_59 retrocopy.
Xenopus tropicalis was not studied using FANTOM5 data.
retro_xtro_59 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 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Xenopus tropicalis | ENSXETG00000025999 | 2 retrocopies |
retro_xtro_47, retro_xtro_59 ,
|