RetrogeneDB ID: | retro_ocun_1203 | ||
Retrocopylocation | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | 3:101476356..101476895(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | CFI | ||
| Ensembl ID: | ENSOCUG00000003892 | ||
| Aliases: | None | ||
| Description: | complement factor I [Source:HGNC Symbol;Acc:5394] |
Retrocopy-Parental alignment summary:
>retro_ocun_1203
GGCCCTGGCACTGTGTGGATGGCCCTGCTCCCGCAGGTTGTGCTTGAGCTCCTGTTCCTCCTCTAGGTCGAGGTCCAAGA
GCAAGCCCAGACTACGGACTTCAGGGCCACCCTGAAGACAGTCAGGTACAGCATCCTCACAATAGACACGAATGCCGCCC
TGGACCTCCTGGGAGGTGAGGACGGGCTGTGCCAGTATAGTGCGGTAACAGATCTAAGACATTCCACCGTTATGGTTATA
AACCCTCCCTGCCAAGTGGATGTGGCTGTCTGTTGTTTGGTGTTGATCTTAACATTGGCATCCCTTCCCTGACAAAGCGC
TGCAACATGTTAGGTGCTATGAGACGTGGCAAAAGCAAGAACGACTGTGATGAAGAGTTCCAGTATTGCTTCTCCAAAGT
CTCCCAGGAGGTGGGGGAAACACTAGGACTGGCTCAGCATGCTCAGGTACGTGAAACAACAGTGGAGCTCCTGTTTGGCA
GCACTATACATTTGTGGGGCAAACCGTACCTGGACAGCCAGCCAGCTACGTGCATGTGC
GGCCCTGGCACTGTGTGGATGGCCCTGCTCCCGCAGGTTGTGCTTGAGCTCCTGTTCCTCCTCTAGGTCGAGGTCCAAGA
GCAAGCCCAGACTACGGACTTCAGGGCCACCCTGAAGACAGTCAGGTACAGCATCCTCACAATAGACACGAATGCCGCCC
TGGACCTCCTGGGAGGTGAGGACGGGCTGTGCCAGTATAGTGCGGTAACAGATCTAAGACATTCCACCGTTATGGTTATA
AACCCTCCCTGCCAAGTGGATGTGGCTGTCTGTTGTTTGGTGTTGATCTTAACATTGGCATCCCTTCCCTGACAAAGCGC
TGCAACATGTTAGGTGCTATGAGACGTGGCAAAAGCAAGAACGACTGTGATGAAGAGTTCCAGTATTGCTTCTCCAAAGT
CTCCCAGGAGGTGGGGGAAACACTAGGACTGGCTCAGCATGCTCAGGTACGTGAAACAACAGTGGAGCTCCTGTTTGGCA
GCACTATACATTTGTGGGGCAAACCGTACCTGGACAGCCAGCCAGCTACGTGCATGTGC
ORF - retro_ocun_1203 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 63.24 % |
| Parental protein coverage: | 89.6 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | GPGAVRMASL---ALLLLLVAAVASQEQAQTTDWRATLKTIRNGVHKIDTYLNAALDLLGGEDGLCQYK- |
| GPG.V.MA.L....L.LL....V..QEQAQTTD.RATLKT.R.....IDT..NAALDLLGGEDGLCQY.. | |
| Retrocopy | GPGTVWMALLPQVVLELLFLL*VEVQEQAQTTDFRATLKTVRYSILTIDT--NAALDLLGGEDGLCQYS< |
| Parental | CRDGSKPFPRYGYKPSPPNGCGSPLFGVHLNIGIPSLTKCCNQHDRCYETCGKSKNDCDEEFQYCLSKIC |
| C...SK.F.RYGYKPS.P.GCG..LFGV.LNIGIPSLTK.CN..........K...D..EEFQYC.SK.. | |
| Retrocopy | CGNRSKTFHRYGYKPSLPSGCGCLLFGVDLNIGIPSLTKRCNMLGAMRRGKSKNDCD--EEFQYCFSKVS |
| Parental | RDVQKTLGLAQHVQACETTVELLFDSVIHLGCKPYLDSQRAACTC |
| ..V..TLGLAQH.Q..ETTVELLF.S.IHL..KPYLDSQ.A.C.C | |
| Retrocopy | QEVGETLGLAQHAQVRETTVELLFGSTIHLWGKPYLDSQPATCMC |
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 | 31 .02 RPM |
| SRP017611_kidney | 0 .00 RPM | 91 .63 RPM |
| SRP017611_liver | 0 .00 RPM | 345 .14 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1203 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1203 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1203 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Oryctolagus cuniculus | ENSOCUG00000003892 | 1 retrocopy |
retro_ocun_1203 ,
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