RetrogeneDB ID: | retro_ocun_1742 | ||
Retrocopylocation | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | GL018838:449889..450334(+) | ||
| 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_1742
ATGCTGTCAGGGAGACAAGTCCTCTGTGACCTCTGGCAGACAAAGGAGACTGGAAACATGGTGTCCATTAAGGCTCTGAA
ATTCTGTCAATTTCAATTATTCAACAACAGTCTCTTTTTTTCCTATATGGTTTGGGCAGTTCTCATGCCAGCTATTACTT
CTGCAAAGTATCAATTTTGATCCTCTTCCGTTTCAAGTAGAGATTCTCAGAGGAGAGTATTTGCACATTCATGAATCACA
GGTCTATTGCCAGGTGAAGTTCTGGTTACCCTTAGGATGTGCAGCTTTTGTGGTAGTCTACATTTTTGGATGCATATTTA
TTTTTTGGCTTCCAAAAGAGAAATATCAATCAAGTATGCGTGACCCAAATAGTGAGTACATGTTCATAGCAACAGTGAAC
ACAGCTAAAAAACCTACACCAACAGAACTCTCTGGCACCTGGGCA
ATGCTGTCAGGGAGACAAGTCCTCTGTGACCTCTGGCAGACAAAGGAGACTGGAAACATGGTGTCCATTAAGGCTCTGAA
ATTCTGTCAATTTCAATTATTCAACAACAGTCTCTTTTTTTCCTATATGGTTTGGGCAGTTCTCATGCCAGCTATTACTT
CTGCAAAGTATCAATTTTGATCCTCTTCCGTTTCAAGTAGAGATTCTCAGAGGAGAGTATTTGCACATTCATGAATCACA
GGTCTATTGCCAGGTGAAGTTCTGGTTACCCTTAGGATGTGCAGCTTTTGTGGTAGTCTACATTTTTGGATGCATATTTA
TTTTTTGGCTTCCAAAAGAGAAATATCAATCAAGTATGCGTGACCCAAATAGTGAGTACATGTTCATAGCAACAGTGAAC
ACAGCTAAAAAACCTACACCAACAGAACTCTCTGGCACCTGGGCA
ORF - retro_ocun_1742 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.47 % |
| Parental protein coverage: | 67.12 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | LLKGEQVLCDLRQTKESGNTVSIKALKFCQYQLFNNSVSF-FLYNLDSSHASYYFCKLS-TFDPPPFQVE |
| .L.G.QVLCDL.QTKE.GN.VSIKALKFCQ.QLFNNS..F.FLY.L.SSHASYYFCK.S..FDP.PFQVE | |
| Retrocopy | MLSGRQVLCDLWQTKETGNMVSIKALKFCQFQLFNNSLFF<FLYGLGSSHASYYFCKVS<NFDPLPFQVE |
| Parental | ILRGEYLHIYESQLCCQLKFWLPIGCAAFAVVYIFGCVFIFWLTKKKYQSSVHDPNSEYMFMAAVNTAKK |
| ILRGEYLHI.ESQ..CQ.KFWLP.GCAAF.VVYIFGC.FIFWL.K.KYQSS..DPNSEYMF.A.VNTAKK | |
| Retrocopy | ILRGEYLHIHESQVYCQVKFWLPLGCAAFVVVYIFGCIFIFWLPKEKYQSSMRDPNSEYMFIATVNTAKK |
| Parental | PTPPELSGTRA |
| PTP.ELSGT.A | |
| Retrocopy | PTPTELSGTWA |
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_1742 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1742 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1742 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,
|