RetrogeneDB ID: | retro_ocun_1371 | ||
Retrocopylocation | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | 7:102569160..102569709(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | ENSOCUG00000025573 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | YIPF2 | ||
| Ensembl ID: | ENSOCUG00000003381 | ||
| Aliases: | None | ||
| Description: | Yip1 domain family, member 2 [Source:HGNC Symbol;Acc:28476] |
Retrocopy-Parental alignment summary:
>retro_ocun_1371
GTCCTTGCTGTCACCGGCAATCTGACCCTGGTGCTGGCCCAGAAGAGGGACCCCTCCATCCACAACAGCCCCCAGTTCCA
CAAAGTGACCGTGGCAGGCATCACCATCTACTGCTATGAGTGGCTCCTGCCGCTGGTGCTGTGGGACTTCCTGCAGTGGC
GCAAGGCCGTTCGGGATCGCGTGGGGCCATACACCTTCCTGGAGACCGTGTATGTCTACGGTTACTCCCTCGTCGTCTGC
ATCCGCACTGTGGTCCTGTGGCTCATCCCTGTGCCGTGGCTGCAATGGCTGTTGGGAGCGCTGGCCCTGATGCTGTCGGC
CGCCGGGCTGGTGTTTACTCTCTGGCCAGTGGTCCGTGAGGACAGCAGGCTGTCGGCCGTGGCGCTGCTGTCCACAGTGG
TGCTGCTGCACGCCCTGCTGGCTACGGGCTGCAAGCTGTACTTCTTCTGCTGCTGTCCCCACAGCCACCCCATGCGGCCA
CCCCATGCCACAGCTCTGGGCGTGAGCACGCTGCTGCCGGCCACGCCGGCCCAGGCCATGGCAACCTCT
GTCCTTGCTGTCACCGGCAATCTGACCCTGGTGCTGGCCCAGAAGAGGGACCCCTCCATCCACAACAGCCCCCAGTTCCA
CAAAGTGACCGTGGCAGGCATCACCATCTACTGCTATGAGTGGCTCCTGCCGCTGGTGCTGTGGGACTTCCTGCAGTGGC
GCAAGGCCGTTCGGGATCGCGTGGGGCCATACACCTTCCTGGAGACCGTGTATGTCTACGGTTACTCCCTCGTCGTCTGC
ATCCGCACTGTGGTCCTGTGGCTCATCCCTGTGCCGTGGCTGCAATGGCTGTTGGGAGCGCTGGCCCTGATGCTGTCGGC
CGCCGGGCTGGTGTTTACTCTCTGGCCAGTGGTCCGTGAGGACAGCAGGCTGTCGGCCGTGGCGCTGCTGTCCACAGTGG
TGCTGCTGCACGCCCTGCTGGCTACGGGCTGCAAGCTGTACTTCTTCTGCTGCTGTCCCCACAGCCACCCCATGCGGCCA
CCCCATGCCACAGCTCTGGGCGTGAGCACGCTGCTGCCGGCCACGCCGGCCCAGGCCATGGCAACCTCT
ORF - retro_ocun_1371 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.05 % |
| Parental protein coverage: | 57.91 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | VLAVTGNLTLVLAQRRDPSIHYSPQFHKVTVAGITIYCYAWLVPLALWGFLRWRKAVRERVGPYTFLETV |
| VLAVTGNLTLVLAQ.RDPSIH.SPQFHKVTVAGITIYCY.WL.PL.LW.FL.WRKAVR.RVGPYTFLETV | |
| Retrocopy | VLAVTGNLTLVLAQKRDPSIHNSPQFHKVTVAGITIYCYEWLLPLVLWDFLQWRKAVRDRVGPYTFLETV |
| Parental | CVYGYSLFVFIPTVVLWLIPVPWLQWMLGALALALSAAGLVFTLWPVVREDSRLAAAALLSTVVLLHTLL |
| .VYGYSL.V.I.TVVLWLIPVPWLQW.LGALAL.LSAAGLVFTLWPVVREDS..............H.LL | |
| Retrocopy | YVYGYSLVVCIRTVVLWLIPVPWLQWLLGALALMLSAAGLVFTLWPVVREDSXXXXXXXXXXXXXXHALL |
| Parental | AMGCKLYFFQPLPPQQVAVPPHATALGVNTLLPATPARATATS |
| A.GCKLYFF...P......PPHATALGV.TLLPATPA.A.ATS | |
| Retrocopy | ATGCKLYFFCCCPHSHPMRPPHATALGVSTLLPATPAQAMATS |
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 | 35 .54 RPM |
| SRP017611_kidney | 0 .00 RPM | 45 .31 RPM |
| SRP017611_liver | 0 .00 RPM | 25 .67 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1371 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1371 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1371 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 | ENSOCUG00000003381 | 1 retrocopy |
retro_ocun_1371 ,
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