RetrogeneDB ID: | retro_rnor_2331 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 6:137050885..137052545(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ipo11 | ||
| Ensembl ID: | ENSRNOG00000039717 | ||
| Aliases: | None | ||
| Description: | importin 11 [Source:MGI Symbol;Acc:MGI:2442377] |
Retrocopy-Parental alignment summary:
>retro_rnor_2331
CTCACCTTCTACCATGTTACCAAGACACTGGCGTCCAAACGCCTGGCTGCTGACAGAAAGCTATTTTATGATTTAGCTTC
TGGAATGTATAATTTTGCCTGTTCTCTGTGGAACCATCATACGGACACATTCCTACAGCAGGTTTCTTCTGGCAATGAGG
CTGCAGTTCTGAGTTCACTAGAGCGAACACTACTGTCGCTAAAAGTGCTGCGGAAGTTAACTCTGAATGGATTTGTGGAA
CCTCATAAGAATATGGAGGTGATGGGTTTTTTACATGGAATATTTGAACGTCTAAAACAGTTTCTGGAGTGCAGCACGAG
TATAGGTACAGACAATGTGTGTCGAGACAGACTGGAGAAGACCATCATCCTTTTCACTAAAGTGCTCTTGGACTTCTTGG
ATCAGCACCCCATTTCATTTACTCCTCTGATTCAGAGGTCACTGGAATTCTCTGTAAGCTATGTTTTTACTGAAGTCGGT
GAAGGCGTTACATTTGAGCGGCCTCATTGTCCAGTGCGTGAATCTTATTAAAATGATTGTCAAAAATTATGCTTATAAGC
CATCCAAAAATTTCGAAGATAGCAGCCCTGAAACACTTGAAGCCCATAAGATTAAGATGGCGTTCTTCACATATCCCACA
TTGACAGAGATATGTCGGCGATTAGTCTCTCATTGTTTTTTATTAACTGAAGAAGAACTGACTATGTGGGAGGAAGATCC
AGAAGGCTTTACAGTGGAAGAAACGGGAGGAGACTCTTGGAAATACAGTTTGAGGCCTTGCACCGAAGTATTATTTATAG
ATATATTCCACGAATATAATCAAACTCTTAGTCCTGTACTTATAGAAATGATGCAAACTCTTCAAGGTCCAACCAATGTA
GAAGATATGAATGCACTGTTAATCAAAGATGCTGTGTATAATGCTGTGGGATTAGCTGCTTTTGAGCTGTCTGACAGTGT
TGACTTTGATCAGTGGTTTAAAACCCAACTTCTTCCAGAATTACAAGTTTCTCATAATAGGTATAAGCCATTACGACGCA
GGGTGATTGGGCTCATTGGTCAGTGGATTTCTGTGAAATTCAAGTCTGACTTGAGACCCAGGCTGTATGAAGCAATCTGT
AACTTGCTTCAAGATCAGGATTTAGTGGTCCGAATTGAAACAGCAACAACTCTGAAGTTAACTGTTGATGATTTTGAATT
TAGGACAGATCAACTTTTACCGTATCTGGAAACCATGTTCGCACTGCTTTTTCAGTTGCTGCAGCAAGTTACAGAATGCG
ATACAAAGATGCATGTTTTGCACGTCCTTTCCTGTGTGATTGAAAGAGTCAATGTACAGATACGGCCGTATGTAGGGTGT
TTGGTGCAGTATTTCCCTCTTCTCTGGAAGCAGAGTGAAGAACACAACATGTTACGATGCGCTATTCTGACAACACATAT
CCATCTTGTTCAGGGACTAGGAGCAGACAGCAAGAACTTGTATCCTTTCCTGCTCCCAGTTATCCAGCTGAGTACCAATG
TTTCCCGGCCTCCACATGTCTACCTTCTGGAAGATGGTCTGGAATTATGGTTAGTGACATTGGAGAACAGCCCATGTGTC
ACACCAGAACTGCTTCGTATATTTCAGAACATGTCACCTCTTCTTGAATTAAGCTCAGAG
ORF - retro_rnor_2331 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.71 % |
| Parental protein coverage: | 77.51 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LTFYHVTKTLASKRLAADRKLFYDLASGIYNFACSLWNHHTDTFLQQVSSGNEAAVLSSLERTLLSLKVL |
| LTFYHVTKTLASKRLAADRKLFYDLASG.YNFACSLWNHHTDTFLQQVSSGNEAAVLSSLERTLLSLKVL | |
| Retrocopy | LTFYHVTKTLASKRLAADRKLFYDLASGMYNFACSLWNHHTDTFLQQVSSGNEAAVLSSLERTLLSLKVL |
| Parental | RKLTVNGFVEPHKNMEVMGFLHGIFERLKQFLECSRSIGTDNVCRDRLEKTIILFTKVLLDFLDQHPISF |
| RKLT.NGFVEPHKNMEVMGFLHGIFERLKQFLECS.SIGTDNVCRDRLEKTIILFTKVLLDFLDQHPISF | |
| Retrocopy | RKLTLNGFVEPHKNMEVMGFLHGIFERLKQFLECSTSIGTDNVCRDRLEKTIILFTKVLLDFLDQHPISF |
| Parental | TPLIQRSLEFSVSYVFTEVGEGVTFER-FIVQCMNLIKMIVKNYAYKPSKNFEDSSPETLEAHKIKMAFF |
| TPLIQRSLEFSVSYVFTEVGEGVTFER..IVQC.NLIKMIVKNYAYKPSKNFEDSSPETLEAHKIKMAFF | |
| Retrocopy | TPLIQRSLEFSVSYVFTEVGEGVTFER>LIVQCVNLIKMIVKNYAYKPSKNFEDSSPETLEAHKIKMAFF |
| Parental | TYPTLTEICRRLVSHYFLLTEEELTMWEEDPEGFTVEETGGDSWKYSLRPCTEVLFIDIFHEYNQTLTPV |
| TYPTLTEICRRLVSH.FLLTEEELTMWEEDPEGFTVEETGGDSWKYSLRPCTEVLFIDIFHEYNQTL.PV | |
| Retrocopy | TYPTLTEICRRLVSHCFLLTEEELTMWEEDPEGFTVEETGGDSWKYSLRPCTEVLFIDIFHEYNQTLSPV |
| Parental | LLEMMQTLQDKGNYLKFNFVLF--SVYNAVGLAAFELFDSVDFDQWFKTQLLPELQVSHNRYKPLRRRVI |
| L.EMMQTLQ...N....N..L....VYNAVGLAAFEL.DSVDFDQWFKTQLLPELQVSHNRYKPLRRRVI | |
| Retrocopy | LIEMMQTLQGPTNVEDMNALLIKDAVYNAVGLAAFELSDSVDFDQWFKTQLLPELQVSHNRYKPLRRRVI |
| Parental | WLIGQWISVKFKSDLRPRLYEAICNLLQDQDLVVRIETATTLKLTVDDFEFRTDQFLPYLETMFTLLFQL |
| .LIGQWISVKFKSDLRPRLYEAICNLLQDQDLVVRIETATTLKLTVDDFEFRTDQ.LPYLETMF.LLFQL | |
| Retrocopy | GLIGQWISVKFKSDLRPRLYEAICNLLQDQDLVVRIETATTLKLTVDDFEFRTDQLLPYLETMFALLFQL |
| Parental | LQQVTECDTKMHVLHVLSCVIERVNIQVMLYV--LISYLNLL-KKAQIHIALACVYIYIYFHLRQGLGAD |
| LQQVTECDTKMHVLHVLSCVIERVN.Q...YV..L..Y..LL.K....H..L.C.......HL.QGLGAD | |
| Retrocopy | LQQVTECDTKMHVLHVLSCVIERVNVQIRPYVGCLVQYFPLLWKQSEEHNMLRCAILTTHIHLVQGLGAD |
| Parental | SKNLYPFLLPVIQLSTDVSQPPHVYLLEDGLELWLVTLENSPCVTPELLRIFQNMSPLLGMSSD |
| SKNLYPFLLPVIQLST.VS.PPHVYLLEDGLELWLVTLENSPCVTPELLRIFQNMSPLL..SS. | |
| Retrocopy | SKNLYPFLLPVIQLSTNVSRPPHVYLLEDGLELWLVTLENSPCVTPELLRIFQNMSPLLELSSE |
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 | 4 .46 RPM | 28 .61 RPM |
| SRP017611_kidney | 2 .86 RPM | 13 .47 RPM |
| SRP017611_liver | 0 .54 RPM | 6 .25 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2331 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2331 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2331 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 | ENSRNOG00000039717 | 1 retrocopy |
retro_rnor_2331 ,
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