RetrogeneDB ID: | retro_xtro_28 | ||
Retrocopy location | Organism: | Xenopus (Xenopus tropicalis) | |
| Coordinates: | GL173205.1:401933..403111(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSXETG00000030588 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_xtro_28
AACCTATATACTATGCAACTACATATTGCCTCACTTAACTTCAAAGGACTTTAATAGTCCACAAAAAAGGAAACTACTAC
TAAATTGGGCTCAAGACTCCAAAATAGATATATTATATATACAGGAAACTCATCTGACTGGTAAGGATCACCCAAAACTG
CTTTCAAAAAACTTTAACAAGACCATTTACACTAACGCTCCCATTAAAAAAAATGGTGTGGCTATCCTATTCAGGAAGTC
CCTTCCTATTAAAATCACTAAGGTCCAAGCAGACAAAAAAGGTAGATTCCTAATTGTTAACTTAGAAGTGTTATCCCAAT
CATTTTTACTAATGAATATTTACGCTCCAAATTTCCATCAAATGGCTTTTATAAACAAACTATTTTGTAAAGTGAAACAA
GAAACCAATGTTAAACTCCTAATTACCAGGGACTTTAACCTGTCTCCCGACCCACTCATAGACAAAGCCCCCACTCCAAA
AGGAAACACCCTAAGAACTGCCACTTGTCTTTCAAAGGCCTTTTTTAAAACTATAAAGCAAATGGAACTATATGATGTAT
TGAGAGCAGGTCACCCTTCTGAGCGTGATTATACTTTTTTTTCACATGTACATTCCTCCTAATTCAAGGATTGATTTAAT
TCTTGCTGATAAGATCTCCTTATTGCAAATGGTCAAATCATATATAGAGATAGCCACCTGGTCGGACCATGCCCCAGTTG
CATGTTTCATAGATTTCCACCAAATTCTCAGCCCGTCCTTTAATTGGAGATTAAACAATACCTTATTACAGAATGAAAAA
CATGCTGAAAAAATAACAAAACTTACCGAGGAATATTTTAACCTGAATCTCTCCCCAGACACCTCTAATGATCTACTTTG
GTGTTCATATAAGGCCTTTATCAGAGGCTATCTAATAGCCATGGCTGCTAAGGAAAAGAAAAAAAGAAACACTAAAGCAG
CAGAGTTACTTGCTATACTAGCCAAAGTTACAAGACAACACAAGCTTCATCCAACTGACGAGCTGGCCCAAAAGGTGGCA
TCCCATAATAAAGAAATAAATGTTTTATGCATGGAAAAAGTTGCATACCAAATACTGCTGACAAAACAACGATACTACAT
AGAAGACAATACTTCTATAGACAAATACTACAGTAAACTATACAACTTAAAAGATGAC
ORF - retro_xtro_28 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.17 % |
| Parental protein coverage: | 97.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | NLYNMQLHIASLNVKGL-NSPQKRKLLLNWAQDSKIDIVCIQEAHLTGKDHPKLISKNFKETIYPNAPIK |
| NLY.MQLHIASLN.KGL.NSPQKRKLLLNWAQDSKIDI..IQE.HLTGKDHPKL.SKNF..TIY.NAPI. | |
| Retrocopy | NLYTMQLHIASLNFKGL>NSPQKRKLLLNWAQDSKIDILYIQETHLTGKDHPKLLSKNFNKTIYTNAPIX |
| Parental | KNGVAILFRNSLPIKIIKVQADKKG-YLIVNLEVLSQPFLLMNLYAPNSHQMTFINIMCNGLLQGESI-- |
| ..GVAILFR.SLPIKI.KVQADKKG..LIVNLEVLSQ.FLLMN.YAPN.HQM.FIN.......Q...... | |
| Retrocopy | XXGVAILFRKSLPIKITKVQADKKGRFLIVNLEVLSQSFLLMNIYAPNFHQMAFINKLFCKVKQETNVKL |
| Parental | -VEMDFNLSPDPLLDKAPTPKGNTLRTATRLSKAFFKTIKQMELYDVWRAGHHSERDYTFFSHVHSS-YS |
| ....DFNLSPDPL.DKAPTPKGNTLRTAT.LSKAFFKTIKQMELYDV.RAGH.SERDY....HVHSS..S | |
| Retrocopy | LITRDFNLSPDPLIDKAPTPKGNTLRTATCLSKAFFKTIKQMELYDVLRAGHPSERDYXXXXHVHSS>NS |
| Parental | RIDLILTDKISLLQMVKSYIGVATWSDHAPVGCFIDFHQIPSPSFSWKLNNTLLQNKIHAEKITKLTEEY |
| RIDLIL.DKISLLQMVKSYI..ATWSDHAPV.CFIDFHQI.SPSF.W.LNNTLLQN..HAEKITKLTEEY | |
| Retrocopy | RIDLILADKISLLQMVKSYIEIATWSDHAPVACFIDFHQILSPSFNWRLNNTLLQNEKHAEKITKLTEEY |
| Parental | FNLNSSPDTPNDLLWCSYKAFIRGHLIAIASKEKKIRNTKLTELIAELAEVTSQHKIHPTGELAQKVTSL |
| FNLN.SPDT.NDLLWCSYKAFIRG.LIA.A.KEKK.RNTK..EL.A.LA.VT.QHK.HPT.ELAQKV.S. | |
| Retrocopy | FNLNLSPDTSNDLLWCSYKAFIRGYLIAMAAKEKKKRNTKAAELLAILAKVTRQHKLHPTDELAQKVASH |
| Parental | NKEINVLNMEKVAYQILLTKQRYYIEDNKNGRLLASKLKDARAD |
| NKEINVL.MEKVAYQILLTKQRYYIEDN.......SKL.....D | |
| Retrocopy | NKEINVLCMEKVAYQILLTKQRYYIEDNTSIDKYYSKLYNLKDD |
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 .14 RPM | 0 .00 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .00 RPM |
| SRP007412_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .00 RPM |
| SRP007412_skeletal_muscle | 0 .00 RPM | 0 .00 RPM |
Xenopus tropicalis was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_xtro_28 retrocopy.
Xenopus tropicalis was not studied using FANTOM5 data.
retro_xtro_28 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 | ENSXETG00000030588 | 2 retrocopies |
retro_xtro_23, retro_xtro_28 ,
|