RetrogeneDB ID: | retro_ocun_1839 | ||
Retrocopylocation | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | GL019231:69729..70292(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | ICOS | ||
| Ensembl ID: | ENSOCUG00000001858 | ||
| Aliases: | None | ||
| Description: | inducible T-cell co-stimulator [Source:HGNC Symbol;Acc:5351] |
Retrocopy-Parental alignment summary:
>retro_ocun_1839
GAATCGCTTTAAGGAGACATCAATGACCCTGCCAAGTATGAGATGTTTACATTTCAGAATGGAGGTGTTCAAATTTTATG
CAAATACCCCGAGATTGTCCTGCAATTCAAAATGCAGCTGCTGACAGGGAGATAAGTCCTCTGTGACTTCAGGCAGACAA
AGGAGAGTGGAAACACGGTGTTCATTAAGGCTCTGAAATTCTGTCAATATCAATTATTCAACAACATTTTCTTTTTTCCT
ATATAATTTGGACAATTCTCATGCCAGCTATTACTTCTGCAAACTATCAATTTTTGACCCTCCTCCTTTTCAAGTAGAGA
TTCTCAGAGGAGAATATTTGCATATTTAGGAATCACAAGCTCTGTTGCCAGGTGAAGTTCTGGTTACCCATAGGATGTGC
AGCTTTTGCAGTAGTCTACATTTTTGAATGCATATTTATTTTTCGGCTTACAAAGGAGAAATATCAATCAAGTGTGCATG
ACCCAAATAGTGAGTATGTGTTCATAGCAGCAGTGAACACAGCTAAAATATCTGCACTGACAGAACTCTCAGGCACCTGG
GCA
GAATCGCTTTAAGGAGACATCAATGACCCTGCCAAGTATGAGATGTTTACATTTCAGAATGGAGGTGTTCAAATTTTATG
CAAATACCCCGAGATTGTCCTGCAATTCAAAATGCAGCTGCTGACAGGGAGATAAGTCCTCTGTGACTTCAGGCAGACAA
AGGAGAGTGGAAACACGGTGTTCATTAAGGCTCTGAAATTCTGTCAATATCAATTATTCAACAACATTTTCTTTTTTCCT
ATATAATTTGGACAATTCTCATGCCAGCTATTACTTCTGCAAACTATCAATTTTTGACCCTCCTCCTTTTCAAGTAGAGA
TTCTCAGAGGAGAATATTTGCATATTTAGGAATCACAAGCTCTGTTGCCAGGTGAAGTTCTGGTTACCCATAGGATGTGC
AGCTTTTGCAGTAGTCTACATTTTTGAATGCATATTTATTTTTCGGCTTACAAAGGAGAAATATCAATCAAGTGTGCATG
ACCCAAATAGTGAGTATGTGTTCATAGCAGCAGTGAACACAGCTAAAATATCTGCACTGACAGAACTCTCAGGCACCTGG
GCA
ORF - retro_ocun_1839 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.63 % |
| Parental protein coverage: | 84.68 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | EVLTGEINDSAKYEMFTFHNGGVQIVCKYPEIVQQFKMQLLKGEQVLCDLRQTKESGNTVSIKALKFCQY |
| E.L.G.IND.AKYEMFTF.NGGVQI.CKYPEIV.QFKMQLL.G..VLCD.RQTKESGNTV.IKALKFCQY | |
| Retrocopy | ESL*GDINDPAKYEMFTFQNGGVQILCKYPEIVLQFKMQLLTGR*VLCDFRQTKESGNTVFIKALKFCQY |
| Parental | QLFNNSVSFF-LYNLDSSHASYYFCKLSTFDPPPFQVEILRGEYLHIYESQ-LCCQLKFWLPIGCAAFAV |
| QLFNN...FF.LYNLD.SHASYYFCKLS.FDPPPFQVEILRGEYLHI.ESQ.LCCQ.KFWLPIGCAAFAV | |
| Retrocopy | QLFNN-IFFF>LYNLDNSHASYYFCKLSIFDPPPFQVEILRGEYLHI*ESQ>LCCQVKFWLPIGCAAFAV |
| Parental | VYIFGCVFIFWLTKKKYQSSVHDPNSEYMFMAAVNTAKKPTPPELSGTRA |
| VYIF.C.FIF.LTK.KYQSSVHDPNSEY.F.AAVNTAK.....ELSGT.A | |
| Retrocopy | VYIFECIFIFRLTKEKYQSSVHDPNSEYVFIAAVNTAKISALTELSGTWA |
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 |
|---|---|---|
| SRP017611_brain | 0 .00 RPM | 0 .17 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .20 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .31 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1839 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1839 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1839 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 10 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Oryctolagus cuniculus | ENSOCUG00000001858 | 10 retrocopies |
retro_ocun_1052, retro_ocun_1545, retro_ocun_1711, retro_ocun_1742, retro_ocun_1748, retro_ocun_1822, retro_ocun_1833, retro_ocun_1839 , retro_ocun_1843, retro_ocun_1867,
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