RetrogeneDB ID: | retro_xtro_14 | ||
Retrocopy location | Organism: | Xenopus (Xenopus tropicalis) | |
| Coordinates: | GL173214.1:129309..130995(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSXETG00000030128 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | XB-GENE-5895314 | ||
| Ensembl ID: | ENSXETG00000007381 | ||
| Aliases: | None | ||
| Description: | hypothetical protein LOC100136946 [Source:Jamboree;Acc:XB-GENE-5895314] |
Retrocopy-Parental alignment summary:
>retro_xtro_14
CTGATTTCAGCGATGGCGGCTGCTGATCTGAGAGACGAGCTGAGCTGCTCCATCTGCCTGAGCATTTATACTGATCCGGT
ATCCCTGCCCTGTGGCCATAACTTCTGCCGGGGCTGCATTGGGGGGGTGCTGGGTATCCAAGAGGGGTCTGGGCGTTATT
CCTGCCCTGAATGCAGAGCTGAGTATCAGGAGTACCCTGCCCTGCCCAGGAACAGAGCTCTGGGGAACATAGCAGAGAGG
TTCCGTCCGACTGAGACAGAGCCGGGGGAGACTGGGATCTTCTGCACTTACTGTCTCCTCTCTCCTGTACCTGCTGCTAA
ATCCTGTCTCCTGTGTGAGGCTTCTCTGTGTGATACCCACCTGAGGGGGCACTGCCAGTCAGCAGAACATGTACTCACTG
AGCCCACCGCTTCCTTTATGGGGAGAAAATGTTCTGTACACAATGAGCCCCTAAAGTATTTCTGCTGGAAGGACTCTGCC
TGTATCTGTGTGTCCTGCTGCCTGGCCGGGGAGCACCGGGGCCACAGGGTGGAGCTGCTGAGTGAGGCCTCTGAGAAGAA
GAAAGAGAAACTGAGGAAAGTTCTGGAGAAACTGAGCCCAGAGAGAGAGGAGACTGAGAGAGGAGCCCAGAGGCTGCAGG
AGCGCAGGAGAGAAGTGGCAGAAGCGGCAGCCGGTGAGACAGAGAGAGTCACTGCCCTGTTTAGGGGCATCAGGGAACAG
CTGGAAGCCCTAGAGAAGCGACTCCTGAGTGACATCTCCAGGCAGAAAGAGGAACTTTGCCTCCAACTCACTGAGCTGAT
CCAACAGCTGGAAATAAAGAAGGATGAGCTGTCCAGGAAGATCCGGCACATTGAGGAGCTGTGCAACATGGCAGATCCAC
TCACTGTCCTACAGGAACAATGGGAATCCCATGGAGCTGCCTTTTGTGGGGCTGAGGGGGCAGATACTGAGGGCAGAGAG
AGAGAGGGTACTGAGGGGGCAGATACTGAGGGCAGAGAGAGAGAGGATACTGAGGGGGCAGATACTGAGGGCAGAGAGAG
AGAGGGTATAAAGGTCCCGGCTGTAGGGGATCTGGATGTGGGTCGGATCTCAGAGACATTACTCACAGGCTTAGCTGGGA
TTGTGACTGGGGTAAAGGGAAGAGTGATCCCTGGGCAGGAGGCTACAGAGCTGGTACTGGATATAAACACGGCTGGGAAT
GGTGTATCTGTATCAGGGGACGGGAAATCTGCTTCCTACTCACTTACAGGCCAGCGTCGCCCACAAACCCCAGAGAGATT
TCAGGTTTATGCTCAGGCTTTAAGCACCAGGAGTTTCCCCTCAGGGCGACATTACTGGGAAGTGGAGGGCAGTGAATCAG
GGAGCTGGAGGGTAGGGGCGGCCTATCCCAGTATAGAGAGGGGAGGGGGTCAGTCCTACATTGGGAATAATAACAAGTCC
TGGGGTTTAATCAGATGGAATAATAACTATACAGTGATACATGACAATAAAGTCACACAGTTACCCCACGCCCCTTCCTG
CAGGAGAATCAGGATCTCATTGGACTATGAGGCTGGACGGCTGTCCTTTTATGAGCTGAGTGAGCCAATCAGGCACTTAC
ACACCTTCACTGCCTCCTTCACTGAGCCCCTTCATGCTGCATTCTGGGTAGGGTGGGATGGTGCCTGGGTGAGAATCAAT
AGTTAG
ORF - retro_xtro_14 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.88 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | YTDPVSLPCGHNFCRGCIGGVLGTQEGSGRYSCPECRGRAEYQERPALPRNRALGNIAERFRPTETEPGE |
| YTDPVSLPCGHNFCRGCIGGVLG.QEGSGRYSCPECR..AEYQE.PALPRNRALGNIAERFRPTETEPGE | |
| Retrocopy | YTDPVSLPCGHNFCRGCIGGVLGIQEGSGRYSCPECR--AEYQEYPALPRNRALGNIAERFRPTETEPGE |
| Parental | TGIFCTYCLLSPVPAAKSCLLCEASLCDTHLRGHCQSAEHVLTEPTTSFMGRKCSVHHKVLEYHCCEGSA |
| TGIFCTYCLLSPVPAAKSCLLCEASLCDTHLRGHCQSAEHVLTEPT.SFMGRKCSVH...L.Y.C...SA | |
| Retrocopy | TGIFCTYCLLSPVPAAKSCLLCEASLCDTHLRGHCQSAEHVLTEPTASFMGRKCSVHNEPLKYFCWKDSA |
| Parental | CICVFCCLAGGHRGHRVELLSKASEKKKKKLRKVLEKLSPEREETERGAQRLQERRGELEEKAAIETERV |
| CICV.CCLAG.HRGHRVELLS.ASEKKK.KLRKVLEKLSPEREETERGAQRLQERR.E..E.AA.ETERV | |
| Retrocopy | CICVSCCLAGEHRGHRVELLSEASEKKKEKLRKVLEKLSPEREETERGAQRLQERRREVAEAAAGETERV |
| Parental | TALFRGIREELEALEKRLLSDISRQKEELSLTLTELIQQLEIKKDELSRKIRHIEELCNMADPLTVLQEQ |
| TALFRGIRE.LEALEKRLLSDISRQKEEL.L.LTELIQQLEIKKDELSRKIRHIEELCNMADPLTVLQEQ | |
| Retrocopy | TALFRGIREQLEALEKRLLSDISRQKEELCLQLTELIQQLEIKKDELSRKIRHIEELCNMADPLTVLQEQ |
| Parental | WESHGAAFCGAKGADNEGRESEDTEGADND-TKGADNEG---RGRE--DIKVPAVGDLDVGRISETLLTG |
| WESHGAAFCGA.GAD.EGRE.E.TEGAD.......D.EG....GRE...IKVPAVGDLDVGRISETLLTG | |
| Retrocopy | WESHGAAFCGAEGADTEGREREGTEGADTEGREREDTEGADTEGREREGIKVPAVGDLDVGRISETLLTG |
| Parental | LAGIVTGVKGRIY-GQEATELVLDINTAGNRVSVSGDGKSASYSRTDQRRPQTPERFQV-SQALSTRSFP |
| LAGIVTGVKGR...GQEATELVLDINTAGN.VSVSGDGKSASYS.T.QRRPQTPERFQV..QALSTRSFP | |
| Retrocopy | LAGIVTGVKGRVIPGQEATELVLDINTAGNGVSVSGDGKSASYSLTGQRRPQTPERFQVYAQALSTRSFP |
| Parental | SGRHYWEVEGSESGGWRVGAAYPSIERVGYQSLIGNNNKSWCLYRGNNNYTVVHDWEVTQLPHVPSCRRI |
| SGRHYWEVEGSESG.WRVGAAYPSIER.G.QS.IGNNNKSW.L.R.NNNYTV.HD..VTQLPH.PSCRRI | |
| Retrocopy | SGRHYWEVEGSESGSWRVGAAYPSIERGGGQSYIGNNNKSWGLIRWNNNYTVIHDNKVTQLPHAPSCRRI |
| Parental | RISLDYEAGRLSFYELSEPIRHLHTFTVSLTEPLHAAFCV-VGGACVRIIS |
| RISLDYEAGRLSFYELSEPIRHLHTFT.S.TEPLHAAF.V...GA.VRI.S | |
| Retrocopy | RISLDYEAGRLSFYELSEPIRHLHTFTASFTEPLHAAFWVGWDGAWVRINS |
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 | 2 .63 RPM | 0 .21 RPM |
| SRP007412_heart | 1 .33 RPM | 0 .13 RPM |
| SRP007412_kidney | 1 .33 RPM | 0 .13 RPM |
| SRP007412_liver | 2 .93 RPM | 1 .41 RPM |
| SRP007412_skeletal_muscle | 0 .62 RPM | 0 .06 RPM |
Xenopus tropicalis was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_xtro_14 retrocopy.
Xenopus tropicalis was not studied using FANTOM5 data.
retro_xtro_14 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 | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000018057 | 1 retrocopy | |
| Xenopus tropicalis | ENSXETG00000007381 | 1 retrocopy |
retro_xtro_14 ,
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