RetrogeneDB ID: | retro_rnor_2353 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 6:39036156..39037111(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rcn1 | ||
| Ensembl ID: | ENSRNOG00000013452 | ||
| Aliases: | Rcn1, Rcn | ||
| Description: | reticulocalbin-1 precursor [Source:RefSeq peptide;Acc:NP_001102056] |
Retrocopy-Parental alignment summary:
>retro_rnor_2353
CTGGGACTCTCCATGGGCTGCTGCTGGCACTGGTGCTGGCGTTCAGGGCCAAGAGCATGATGAGCAAGGAGCACATAGTT
TGTCCCGATTCAGAGCTGGGCCAGTGGCCACCAGAGGACAAGCACAGCTTCCTGTACGATCATGAGGTCTTCCTGGGCAA
GGAGGACTCCAAGACCTTTGATAGCTAAGCCTGGATGAGAGCAAGGAGAGGCTGGGGAAAATTGTTGATTCAATTGACAG
TGATGGAGGCAGCCTTGTTACTACTGAGCAGCTGAAAGTTTGGATCAAACAGGTACAAAAAAGATACATCTACCATAATG
TGGCTAAACTCTGGAAGGATTATGATAGGGACATAGACGAAAAGATCTCCTGGGAAGAATACAAGCAGTCTACTTTTGGC
TACTACCTGGGAAACCTTGCTGAATCCCAAGATAGCTCTGATCTTCACACCTTTAAAAAAATGCCTCCATGAGATGAGAG
GAGGTTTAAGGCTTCAGACATTGACAGCAACCTTACAGCTACTCGAGAGGGATTCATTGCTTTCTGAACCCAGAGGAGTT
GAAACATATGAAGGAGATTGTAGTTCTGGAAACCCTGGAGGATATCGACAAGAACAGGGAAGGACTTGTGGACCAGGATG
AGTATATTGTGGACATGTTTTTCCCACGAGGACAATGCCCCTGAGCCAGACTGGGTTTTGTCCAAATGGGAGCAGTTCAA
TGATTTCCCAGATCTGAACAAGGATGGGAAGCTGGACAAGGATGAGATTCACCACTGAATCCTCCCTCACAACTATGACC
ATGCAGGGGCTGAGGCCCGGCGTCTGGTGTATGAGTCAGATAAAAACAAGGATGAGATGCTAACCAAGGAGGAGATTCTA
CAAAACTGGAACATGTTTGTGGGAAGTCAAGCCATCAATTACAAGGAAGATCTTACCAAAAATCGTGATGAACTT
ORF - retro_rnor_2353 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.5 % |
| Parental protein coverage: | 98.15 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | LGLALG-LLLALVLALRAKPTVRKERVVRPDSELGERPPEDNQSFQYDHEAFLGKEDSKTFDQ-LSPDES |
| LGL..G.LLLALVLA.RAK....KE..V.PDSELG..PPED..SF.YDHE.FLGKEDSKTFD..LS.DES | |
| Retrocopy | LGLSMG<LLLALVLAFRAKSMMSKEHIVCPDSELGQWPPEDKHSFLYDHEVFLGKEDSKTFDS<LSLDES |
| Parental | KERLGKIVDRIDSDGDGLVTTEELKVWIKRVQKRYIYDNVAKVWKDYDRDKDEKISWEEYKQATYGYYLG |
| KERLGKIVD.IDSDG..LVTTE.LKVWIK.VQKRYIY.NVAK.WKDYDRD.DEKISWEEYKQ.T.GYYLG | |
| Retrocopy | KERLGKIVDSIDSDGGSLVTTEQLKVWIKQVQKRYIYHNVAKLWKDYDRDIDEKISWEEYKQSTFGYYLG |
| Parental | NPAEFQDSSDHHTFKKMLPRDERRFKASDLDGDLTATREEFTA-FLHPEEFEHMKEIVVLETLEDIDKNG |
| N.AE.QDSSD.HTFKKM.P.DERRFKASD.D..LTATRE.F.A.FL.PEE..HMKEIVVLETLEDIDKN. | |
| Retrocopy | NLAESQDSSDLHTFKKMPP*DERRFKASDIDSNLTATREGFIA<FLNPEELKHMKEIVVLETLEDIDKNR |
| Parental | DGFVDQDEYIADM-FSHEDNGPEPDWVLSEREQFNDFRDLNKDGKLDKDEIRHWILPQDYDHAQAEARHL |
| .G.VDQDEYI.DM.FSHEDN.PEPDWVLS..EQFNDF.DLNKDGKLDKDEI.H.ILP..YDHA.AEAR.L | |
| Retrocopy | EGLVDQDEYIVDM>FSHEDNAPEPDWVLSKWEQFNDFPDLNKDGKLDKDEIHH*ILPHNYDHAGAEARRL |
| Parental | VYESDKNKDEMLTKEEILDNWNMFVGSQATNYGEDLTKNHDEL |
| VYESDKNKDEMLTKEEIL.NWNMFVGSQA.NY.EDLTKN.DEL | |
| Retrocopy | VYESDKNKDEMLTKEEILQNWNMFVGSQAINYKEDLTKNRDEL |
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 | 46 .66 RPM |
| SRP017611_kidney | 0 .00 RPM | 28 .40 RPM |
| SRP017611_liver | 0 .00 RPM | 8 .94 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2353 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2353 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2353 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 31 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000049449 | 2 retrocopies | |
| Pongo abelii | ENSPPYG00000003385 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000013452 | 28 retrocopies |
retro_rnor_1207, retro_rnor_1224, retro_rnor_2111, retro_rnor_2112, retro_rnor_2113, retro_rnor_2352, retro_rnor_2353 , retro_rnor_2354, retro_rnor_2355, retro_rnor_2408, retro_rnor_2409, retro_rnor_2410, retro_rnor_2434, retro_rnor_2435, retro_rnor_2436, retro_rnor_2437, retro_rnor_2438, retro_rnor_2486, retro_rnor_2508, retro_rnor_2509, retro_rnor_2510, retro_rnor_2511, retro_rnor_2513, retro_rnor_2664, retro_rnor_2711, retro_rnor_2716, retro_rnor_2760, retro_rnor_797,
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