RetrogeneDB ID: | retro_ocun_848 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | 15:86561369..86562580(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TSR1 | ||
| Ensembl ID: | ENSOCUG00000014256 | ||
| Aliases: | None | ||
| Description: | TSR1, 20S rRNA accumulation, homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:25542] |
Retrocopy-Parental alignment summary:
>retro_ocun_848
ACCAGTTACCAAGCTGAATGGATTTCGGACGAAGATGGTGACATGGTGGGGAAGGAGATGAATGTGATGATACAGAACAT
GAGGAATTTTTGGATGGGGAATTTCAGAATAAGAGGGTGAAGTGGAAGAAGAGAAAGAATGTGTGAAACTATGACCAGAG
GGGACTCTGTAAGTGATGATGATCTGCATGATGAGAAAGTAGATGAAGAGGCTGAGGAAAAAATGGCAAAGTAGAAACTA
GAAAGACTCAAAGAGATGTTTCCAGGTACGTGGAAACCACCCCATGATGTGGCTGCCAGAATTTGATTTCAGAAATACAG
AGGTCTTAGGAGCTTCCAGACTTTTCGATGGGATCCTCAGAAAAACCTTCCTCAAGATTATACTCAGATCTTTCATTTTC
ACAACTTTACTAATCCTGGGAAAGGCATCTTGAGGGAGATTGATGAAGAGGTAGAAGGAGGTGAGGTTGGCTGGTGTGTC
ACACGTCACGTCTCTGATGTTCCTGTCTCAGTGGTGGAGCCCTTCAGGTGAGGAGCATTTGTAATCGCATTTTCTTTACT
CCCTCATCAACAGAAGATGTCAGTATTGAATACAGTGGTGAGGCAGGACCCTGGAGACACCGAACCTGTGAAAGCCAAAG
GGGAACTATCTTCCACTGTAGGTTCAGGTGCTTCTGAGCCTCTCTTTTATTCTCTCAGCACATTGCAGCAGGTAAACATA
AATTTCAGAGATTTCTAACTGCTGATGTGGACCTTGTGGTCATAGTATATATGCCAATCACTTTTCTTTCTGCATCTGTG
CTGCTTTTCAAACAGAAAAACAATGGGCACCTCATTGCTACAGGCCATCTGTCGTCGGTGGATCCAGACAGAATGGTCAT
CGAGAGAGTTGTTCTGAGTGGTTATCCTTTTAAAGGTTTTATGAAGATGGCAGTAGTGAGTCACATGTTCTTCAATAGAG
AGGATGTGCTGTGGTTTAAACCAGTGGAACTGAGAACAAAGTGGAGCTGAAGGAGACACATCAAAGAGCCTTTAGGTACC
TATGGCCACATGAAGTGCAGTTTTGATGGGAAGCTAAAATCTCAAGACATAGTAATGATGAACCTCTATCAATGAGTTCT
CTCCAAATGGACTTAGGATCTATATGTAGCAGAACCAGTACCTTGGGTAAAAAGTGAGATTTTTTTATCAGCGCTTGAAA
TGGACCCAGAA
ORF - retro_ocun_848 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 72.99 % |
| Parental protein coverage: | 50.43 % |
| Number of stop codons detected: | 7 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | SSYQAEWILDEDGDS-GGEGDEYDDTEHEDFMEEESQDESSEVEE-EEECETMTVGDSVRDD-LYDENVD |
| .SYQAEWI.DEDGD..GGEGDE.DDTEHE.F...E.Q.........E..CETMT.GDSV.DD.L.DE.VD | |
| Retrocopy | TSYQAEWISDEDGDM<GGEGDECDDTEHEEFLDGEFQNKRVKWKK>ERMCETMTRGDSVSDDDLHDEKVD |
| Parental | EEAEEKMLEKYKQERLEEMFPDEVDTPRDVAARIRFQKYRGLKSFRTSPWDPKENLPRDYARIFQFQNFA |
| EEAEEKM..K.K.ERL.EMFP.....P.DVAARI.FQKYRGL.SF.T..WDP..NLP.DY..IF.F.NF. | |
| Retrocopy | EEAEEKMA-K*KLERLKEMFPGTWKPPHDVAARI*FQKYRGLRSFQTFRWDPQKNLPQDYTQIFHFHNFT |
| Parental | NTRKSIFKEIDDKEVEGAEVGWYVTLHVSDVPVSVVESFRRGAPMIAFSLLPHEQKMSVLNMVVRRNPGD |
| N..K.I..EID..EVEG.EVGW.VT.HVSDVPVSVVE.FR.GA..IAFSLLPH.QKMSVLN.VVR..PGD | |
| Retrocopy | NPGKGILREIDE-EVEGGEVGWCVTRHVSDVPVSVVEPFR*GAFVIAFSLLPHQQKMSVLNTVVRQDPGD |
| Parental | TEPVKAKEEL-IFHCGFRRFRASPLFSQHTAADKHKFQRFLTADVALVVTVYAPITFPPASVLLFKQKSN |
| TEPVKAK.EL.IFHC.FR.F.AS.LFSQH.AA.KHKFQRFLTADV.LVV.VY.PITF..ASVLLFKQK.N | |
| Retrocopy | TEPVKAKGEL<IFHCRFRCF*ASLLFSQHIAAGKHKFQRFLTADVDLVVIVYMPITFLSASVLLFKQKNN |
| Parental | GMHNLIATGHLLSVDPDRMVIKRVVLSGHPFKIFTKTAVVRYMFFNREDVLWFKPVELRTKWGRRGHIKE |
| G...LIATGHL.SVDPDRMVI.RVVLSG.PFK.F.K.AVV..MFFNREDVLWFKPVELRTKW..R.HIKE | |
| Retrocopy | G--HLIATGHLSSVDPDRMVIERVVLSGYPFKGFMKMAVVSHMFFNREDVLWFKPVELRTKWS*RRHIKE |
| Parental | PLGTHGHMKCSFDGKLKSQDTVLMNLYKRVFPKWTYDPYVPEPVPWIKSEIPSTVLEMDPE |
| PLGT.GHMKCSFDGKLKSQD.V.MNLY..V..KWT.D.YV.EPVPW.KSEI....LEMDPE | |
| Retrocopy | PLGTYGHMKCSFDGKLKSQDIVMMNLYQ*VLSKWT*DLYVAEPVPWVKSEIFLSALEMDPE |
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 | 39 .74 RPM |
| SRP017611_kidney | 0 .00 RPM | 47 .03 RPM |
| SRP017611_liver | 0 .00 RPM | 25 .28 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_848 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_848 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_848 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000019273 | 1 retrocopy | |
| Cavia porcellus | ENSCPOG00000014833 | 2 retrocopies | |
| Oryctolagus cuniculus | ENSOCUG00000014256 | 1 retrocopy |
retro_ocun_848 ,
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