RetrogeneDB ID: | retro_rnor_1349 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 18:40831949..40832779(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Arfip2 | ||
| Ensembl ID: | ENSRNOG00000018440 | ||
| Aliases: | Arfip2, POR | ||
| Description: | Arfaptin-2 [Source:UniProtKB/Swiss-Prot;Acc:Q6AY65] |
Retrocopy-Parental alignment summary:
>retro_rnor_1349
TCTGGTGATGGACCCACAGGGTCTGGTCACCAACCATCTTCTGGCCCTAGTGATAAGGTGGCCCAGGGGGTATCACTGGA
GAAGTGTTTAAAATCATCAAGAAATGGAGCATCAACACATAAGTGCACAAAGCAGCTGTTATCAGAGAGATGTGGCCGAG
GCTCCCCAACTGTGGATATGGACCTAGAGTTGCAGATTGAGTTGTTGTGTGAGACGAAGCCCAAAAATGAAAGTGTCCTG
CATCTGAGTTGGCCACCTATAGCCCACCTCTACAGCCTGCTGCAGGCACAGCATGTACTAGGTGACTTCTTTGCTGACCT
CAGTCAGAAGTTCCTGGAGCTTCAGGAGGAATTTGGCTATAATGCAGAGATGGTGAAGCTGTGGTACAAGAATGGGGAGA
CACTATGAGGGGCTGGGAACTTCTTTGTCTCTTGCATGAGCACACTGGTCAGCATGACCATGGAAGCCACACTCATGACT
GTCAAACAGTACGAGGCTGCAAGGCTAGAATATGATGCCTACTGGACAGACTTAAAGGAGCTGAGCCTATGCCCCTGGAA
TGCAGGAATGCAGTGTTGACTGGGGAGTACCCAGGCCACTTTCCAGACCCATTGAGACAAACATGAGAAGCTGCAGGGAG
TTATGCCCATCAAACAGCCCAACTTCCTGAGAGAAAACAAGATCAAGTTGATCTATAGCAACTGCTCTTCAACAGTGCAG
TGTCTGCCTACTTTGCTGCGAACCAGAAACAATGGAAGCAGATCCTGCAGCAGTTCAACATTCAACTACGGCCTCCAGGA
GCCAAGAAGGCTTCCTGGATAGAGGCACAG
ORF - retro_rnor_1349 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 66.31 % |
| Parental protein coverage: | 81.23 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | TGSGRHPSHSTSPSGPGDEVARGIAGEKFDIVKKWGINTYKCTKQLLSERFGRGSRTVDLELELQIELLR |
| .G.G...S.....SGP.D.VA.G...EK.......G..T.KCTKQLLSER.GRGS.TVD..LELQIELL. | |
| Retrocopy | SGDGPTGSGHQPSSGPSDKVAQGVSLEKCLKSSRNGASTHKCTKQLLSERCGRGSPTVDMDLELQIELLC |
| Parental | ETKRKYESVLQLGRALTAHLYSLLQTQHALGDAFADLSQKSPELQEEFGYNAETQKLLCKNGETLLGAVN |
| ETK.K.ESVL.L.....AHLYSLLQ.QH.LGD.FADLSQK..ELQEEFGYNAE..KL..KNGETL.GA.N | |
| Retrocopy | ETKPKNESVLHLSWPPIAHLYSLLQAQHVLGDFFADLSQKFLELQEEFGYNAEMVKLWYKNGETL*GAGN |
| Parental | FFVSSINTLVTKTMEDTLMTVKQYEAARLEYDAYRTDLEELSLGPRDAGTRGRLESAQATFQTHRDKYEK |
| FFVS...TLV..TME.TLMTVKQYEAARLEYDAY.TDL.ELSL.P..AG....L.S.QATFQTH.DK.EK | |
| Retrocopy | FFVSCMSTLVSMTMEATLMTVKQYEAARLEYDAYWTDLKELSLCPWNAGMQC*LGSTQATFQTH*DKHEK |
| Parental | LRGDVAIKL-KFLEENKIKVMHK-QLLLFHNAVSAYFAGNQKQLEQTLQQFNIKLRPPGAEKPSWLEEQ |
| L.G...IK...FL.ENKIK.....QL.LF..AVSAYFA.NQKQ..Q.LQQFNI.LRPPGA.K.SW.E.Q | |
| Retrocopy | LQGVMPIKQPNFLRENKIKLIYS<QL-LFNSAVSAYFAANQKQWKQILQQFNIQLRPPGAKKASWIEAQ |
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 | 55 .65 RPM |
| SRP017611_kidney | 0 .00 RPM | 44 .94 RPM |
| SRP017611_liver | 0 .00 RPM | 23 .00 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_1349 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_1349 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_1349 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 | |
|---|---|---|---|
| Rattus norvegicus | ENSRNOG00000018440 | 1 retrocopy |
retro_rnor_1349 ,
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