RetrogeneDB ID: | retro_rnor_20 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | X:29913532..29914930(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSRNOG00000025637 | |
| Aliases: | LOC317471, Fam154a | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Fam154a | ||
| Ensembl ID: | ENSRNOG00000048197 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_rnor_20
ATGGCTCTCATGAATAGGAAGTGCATTTGTGACCTTTGCTCTTGTGGCAAGCATCACTGCCCACATCTCCCTACCAAGAT
TTATGAGAAGACAGAGAAACCATGTTTCTTCTCCGAATACACCGAGAAGTATCCTACCTATCTTTCTTATGTGCCCCGAG
AGTCCTTCAAACCCAAGTTGGAGTACCAGAAAGTAAATATACCAATGGAAGGCCTGTCCACAACGAAGAGAGACTTTGGA
ACCTTCAACATAGTACCAGTGAAACACCATCTTCCTGAGAAGGCCACTCCAATCCAAGACGAAATGGATTTCCTCACAAC
GTATAATCAACACTACAACTACTGCCCTGCCAATCGAGTGAACCCCATCAAACCTCGAGACAACAAACATCAATGTAATG
ACAAAATGGAGTGTGTGCCTACGTACAAAGCTGATTATTTGCCCTGGAACCAACAAAAGAGATCTTCGATTCGTCCACCA
CAATCATACCGTCCTGCGTCCTGTAGGTTTGATCATAGAACCACACACCAGGACGATTATCCCATAAAAAATCCTGTGGA
TACTGTGAGTTACAAACCTCCACATGGGCCCAAGCTGTGCAACATCCCCTTGGAGAGTATGACAAGTTACAAATCGAGCT
ATGTGGCCCATCCCATGGAGAAGCGGTGTGTGTATGAGGGAGAGAAGTATAAACCAAGTGAAGTCCCTTTTGATAGCCTT
ACCACCCACAAAGATTCCTACAGGGGTTTGATCGGGGAGCCTGCCAAGACCTGGAAACCTGCCCCAAATCACCCTGGGCT
GGATATACCTTTTCCATCCAACACTGAATTCCGAGAAAAATTCCAACCTTGGCCAACACCCAAGATTGTCCCCAAAGAGT
CCATTGCCTACATCCCTCCTGAAGGGAAGATGGATCTTCTAACAACTGTGCAAGCAGACTACAAGTGCCCCAATGGTGTT
CCTGCTCAGTCCTGCCGGCCAGTCATCCATTTGAAGAAGAGTGACCGATTTGAAAGCTCTACGACCAACAGAGAGGATTT
TAAACACTGGGCCAACATCCGAAGAGAGCCAGTCAAACCTAATCACCAGCTGAAATTCTCTGATGAACCTATGGAATACA
TGACCACCAATCGTGCCCACTATGTGCCTCATGCACCAGCCAATACCAAAAGCTGCAAGCCAACCTGGTCTGGCCCTCGT
GTAAACATCCCTTTAGAAGGCCAGACCACCTACTCTACCAGTTTTACTCCTAAGGAAATTCAAAGGTGCCCAGCTTCATA
CCCTGAACCCCCTGGCTACATCTTTGATGAGGTGGATGCTGTAGGGCACAGGCTGTACAGGCCGGCTTCCGGAGCAACTT
CTCAAGAGAGCAACCATCTTGGCTTTGGTGATGCATAA
ORF - retro_rnor_20 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 56.32 % |
| Parental protein coverage: | 97.2 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | CRRHRCPHLPTKIYDKTEKPSLLSEYTENYPIYESYLPRNSFKPECAYQKASIPMEGLTTSRRDFGLHKM |
| C..H.CPHLPTKIY.KTEKP...SEYTE.YP.Y.SY.PR.SFKP...YQK..IPMEGL.T..RDFG.... | |
| Retrocopy | CGKHHCPHLPTKIYEKTEKPCFFSEYTEKYPTYLSYVPRESFKPKLEYQKVNIPMEGLSTTKRDFGTFNI |
| Parental | LPVKFYQPAAYVPSQESMNLLTSYKHDFNYIPTCPVGLIKPRDSKFPNGDKTVQYLPTYKVDYVPWNQPR |
| .PVK...P....P.Q..M..LT.Y....NY.P...V..IKPRD.K....DK.....PTYK.DY.PWNQ.. | |
| Retrocopy | VPVKHHLPEKATPIQDEMDFLTTYNQHYNYCPANRVNPIKPRDNKHQCNDK-MECVPTYKADYLPWNQQK |
| Parental | RELLRPPHKYRPESAKFENRTTHQDDYTMKCLVTTESCKPSVKAKICNIPLEDLTNYKMSYVPHPVEKRF |
| R...RPP..YRP.S..F..RTTHQDDY..K..V.T.S.KP....K.CNIPLE..T.YK.SYV.HP.EKR. | |
| Retrocopy | RSSIRPPQSYRPASCRFDHRTTHQDDYPIKNPVDTVSYKPPHGPKLCNIPLESMTSYKSSYVAHPMEKRC |
| Parental | VKEAEKYIPCDIPFENLTTHKESYRGLLGEPAKSSKPPGKIPVHDVPFSDITEIQEKYQAWPTPQIVPKA |
| V.E.EKY.P...PF..LTTHK.SYRGL.GEPAK..KP....P..D.PF...TE..EK.Q.WPTP.IVPK. | |
| Retrocopy | VYEGEKYKPSEVPFDSLTTHKDSYRGLIGEPAKTWKPAPNHPGLDIPFPSNTEFREKFQPWPTPKIVPKE |
| Parental | PVVYVPPEEKMDLLTTVQTHYKHRKGSPAITCRPVPSIKKSGRFQSSTTSKDDFKQWAAVNTKPIRPVPH |
| ...Y.PPE.KMDLLTTVQ..YK...G.PA..CRPV...KKS.RF.SSTT...DFK.WA.....P..P... | |
| Retrocopy | SIAYIPPEGKMDLLTTVQADYKCPNGVPAQSCRPVIHLKKSDRFESSTTNREDFKHWANIRREPVKPNHQ |
| Parental | LNLPVEPLDCQTTTKICYVPHPPTITENYKPAWVGPRRNIPVEGQTTYSISFTPKDLGRCPASYINPPGY |
| L....EP....TT....YVPH.P..T...KP.W.GPR.NIP.EGQTTYS.SFTPK...RCPASY..PPGY | |
| Retrocopy | LKFSDEPMEYMTTNRAHYVPHAPANTKSCKPTWSGPRVNIPLEGQTTYSTSFTPKEIQRCPASYPEPPGY |
| Parental | IFEEVDSTGHKIYRSISQTASRQNSSLSIHD |
| IF.EVD..GH..YR..S...S.....L...D | |
| Retrocopy | IFDEVDAVGHRLYRPASGATSQESNHLGFGD |
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 .00 RPM |
| SRP017611_kidney | 0 .07 RPM | 0 .00 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .00 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_20 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_20 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_20 has 1 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Mus musculus | retro_mmus_3727 |
Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000028492 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000048197 | 1 retrocopy |
retro_rnor_20 ,
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