RetrogeneDB ID: | retro_rnor_1927 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 3:151596012..151596579(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Nipa1 | ||
| Ensembl ID: | ENSRNOG00000042702 | ||
| Aliases: | Nipa1, Spg6 | ||
| Description: | magnesium transporter NIPA1 [Source:RefSeq peptide;Acc:NP_001100989] |
Retrocopy-Parental alignment summary:
>retro_rnor_1927
ATGGCTGTTGGCCAGATTGGAAACTTCCTAGTTTACACTGCAAACCCTAAGGTGCCGGTGACTCCAATAGGTGCTCTGGG
GATACCATTTGGGTCCATTTTAGCTTCTTATTGTCTGAAGGAAAAACTCAACATCTTGGGCATGTTGGGGAGTCTGCTAG
GCTGTACAGATTCACTCATACTGATTATCCTTCTCAGAAGTCTGAGAGTATGACAACTCGGTGTGAGTTGGAGGAAAAGC
TGACCAATCCAGTGTTTGTGGGCTACCTGTGCATTGTGCTGTTCATGATGCTGCTGTTGATCTTTGGATTGCCCCAGTCC
ACGTGCCCACCAACATCATGGTCTATGCCAGCATCTCTTCTTTGTTGGGGAGTTTCATTGTGCCTTCTACCAAGGGCATT
GGCCTGGCAGCCCAAGACATCTTTCACAACAAGCCGTTGAGTCAGAGAACCCTCTGTCTGAACCAGGTACTCCTGGCTGT
CCTGGGCTGCAGCACCATTACCCAATTCAGGTACATCAACAAGGCTTGGAGTGCTTCAACTCATCTGTCTTTTGGGCCAT
CTATTAC
ORF - retro_rnor_1927 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.27 % |
| Parental protein coverage: | 70.37 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MAVGQIGNFLAYTAVPTVLVTPLGALGVPFGSILASYLLKEKLNILGKLGCLLSCAGSVVLII-HSPKSE |
| MAVGQIGNFL.YTA.P.V.VTP.GALG.PFGSILASY.LKEKLNILG.LG.LL.C..S..LII..S.KSE | |
| Retrocopy | MAVGQIGNFLVYTANPKVPVTPIGALGIPFGSILASYCLKEKLNILGMLGSLLGCTDSLILII<PSQKSE |
| Parental | SVTSQAELEEKLTNPVFVGYLCIVLLMLLLLIF-WIAPAHGPTNIMVYISICSLLGSFTVPSTKGIGLAA |
| S.T...ELEEKLTNPVFVGYLCIVL.M.LLLIF.WIAP.H.PTNIMVY.SI.SLLGSF.VPSTKGIGLAA | |
| Retrocopy | SMTTRCELEEKLTNPVFVGYLCIVLFMMLLLIF<WIAPVHVPTNIMVYASISSLLGSFIVPSTKGIGLAA |
| Parental | QDILHNNPSSQRALCLCLVLLAVLGCSIIVQFRYINKA-LECFDSSVFGAIYY |
| QDI.HN.P.SQR.LCL..VLLAVLGCS.I.QFRYINKA.LECF.SSVF.AIYY | |
| Retrocopy | QDIFHNKPLSQRTLCLNQVLLAVLGCSTITQFRYINKA<LECFNSSVFWAIYY |
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 | 35 .30 RPM |
| SRP017611_kidney | 0 .00 RPM | 11 .51 RPM |
| SRP017611_liver | 0 .00 RPM | 4 .91 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_1927 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_1927 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_1927 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ornithorhynchus anatinus | ENSOANG00000031286 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000042702 | 1 retrocopy |
retro_rnor_1927 ,
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