RetrogeneDB ID: | retro_ocun_1535 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | AAGW02079214:53729..54571(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | UHMK1 | ||
| Ensembl ID: | ENSOCUG00000012411 | ||
| Aliases: | None | ||
| Description: | U2AF homology motif (UHM) kinase 1 [Source:HGNC Symbol;Acc:19683] |
Retrocopy-Parental alignment summary:
>retro_ocun_1535
TCCAGAGATGTTCTGGAAGGCCTTGCTCTCCTTCATCATGAGGGTCGTGTCCACGCAGACCTCAAACCGCAGAACATACT
GTGGAGTGCAGAGAACGAATGTTTTAAACTCACTGACTTTGGACTTAGCTTCAAAGAAGGCACTCCGGGTGTAAAGTACA
TTCAAACAGACGGGTGTCGTGCTCCAGAAGCAGAGCTGAAAAATCACGTGGCCCAGGCTGGCCTGCAGAGTGATACATAA
TGTAGCTCGGCTGCTGGTCTGCGGAGCCTAGGAATCATTTTACTGGAAATGTTCTCAGGAACGAAGCTGAAGCATACAGT
CCGATCTCAGGAATGGAAGGCAAGCAGTTCTGCTGTTGTTGATGAGATATTTGCCGGTAAAGCAGTGGTGAATGCCACAA
TTCCAACCCGTCACCTAAGAGACCTTATCAAAAGCATGCTTCATGATGATCCAAGCAGAAGAGTTCCTGCTGAAATGGCA
TCGCGCAGCCCATTCGTTAGCATTCCTTTTGCCCCTCATGTTGAAGATCTGATGGTAGTTCCTACCCCACTGCTAAGACT
GCTGAGCATGCTAGATGATGATCATCTTGAGAATGAAGAGGAACATGAAGATATTGTAGAAGATGTAAAAGAGGAATGCC
AGAAATATGGACCCGTGATATCTCTGCTTGTCCAAAGGAAAATCCTGGCAGAGGGCAAGTCTTTGTCGAGTATGCCAATG
CTGGTGGTTCCAAAGATGCTCAGGAATTACTGACCGGAAGGATGTTTGATGGGAAGTTTGTCATGGCTACATTCTACCCG
CAGAGTGCCTACAAGAGGGGATATCTGTATCAAACCTTGCTT
ORF - retro_ocun_1535 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.33 % |
| Parental protein coverage: | 67.06 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | ARDVLEALAFLHHEGYVHADLKPRNILWSAENECFKLIDFGLSFKEGNQDVKYIQTDGYRAPEAELQNCL |
| .RDVLE.LA.LHHEG.VHADLKP.NILWSAENECFKL.DFGLSFKEG...VKYIQTDG.RAPEAEL.N.. | |
| Retrocopy | SRDVLEGLALLHHEGRVHADLKPQNILWSAENECFKLTDFGLSFKEGTPGVKYIQTDGCRAPEAELKNHV |
| Parental | AQAGLQSDTECTSAVDLWSLGIILLEMFSGMKLKHTVRSQEWKANSSAIIDHIFASKAVVNAAIPAYHLR |
| AQAGLQSDT.C.SA..L.SLGIILLEMFSG.KLKHTVRSQEWKA.SSA..D.IFA.KAVVNA.IP..HLR | |
| Retrocopy | AQAGLQSDT*CSSAAGLRSLGIILLEMFSGTKLKHTVRSQEWKASSSAVVDEIFAGKAVVNATIPTRHLR |
| Parental | DLIKSMLHDDPSRRIPAEMALCSPFFSIPFAPHIEDLVMLPTPVLRLLNVLDDDYLENEEEYEDIVEDVK |
| DLIKSMLHDDPSRR.PAEMA..SPF.SIPFAPH.EDL...PTP.LRLL..LDDD.LENEEE.EDIVEDVK | |
| Retrocopy | DLIKSMLHDDPSRRVPAEMASRSPFVSIPFAPHVEDLMVVPTPLLRLLSMLDDDHLENEEEHEDIVEDVK |
| Parental | EECQKYGPVVSLLV-PKENPGRGQVFVEYANAGDSKAAQKLLTGRMFDGKFVVATFYPLSAYKRGYLYQT |
| EECQKYGPV.SLLV.PKENPGRGQVFVEYANAG.SK.AQ.LLTGRMFDGKFV.ATFYP.SAYKRGYLYQT | |
| Retrocopy | EECQKYGPVISLLV<PKENPGRGQVFVEYANAGGSKDAQELLTGRMFDGKFVMATFYPQSAYKRGYLYQT |
| Parental | LL |
| LL | |
| Retrocopy | LL |
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 .55 RPM | 6 .79 RPM |
| SRP017611_kidney | 1 .32 RPM | 5 .37 RPM |
| SRP017611_liver | 0 .15 RPM | 2 .77 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1535 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1535 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1535 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000001048 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000012411 | 3 retrocopies |
retro_ocun_1245, retro_ocun_1535 , retro_ocun_1547,
|
| Rattus norvegicus | ENSRNOG00000002941 | 1 retrocopy |