RetrogeneDB ID: | retro_rnor_946 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 13:2205077..2205532(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Lasp1 | ||
| Ensembl ID: | ENSRNOG00000004132 | ||
| Aliases: | None | ||
| Description: | LIM and SH3 domain protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q99MZ8] |
Retrocopy-Parental alignment summary:
>retro_rnor_946
ATGAACCATAATTGTGCTTGGTGCAGCAAGACCGTGTACCCTATGTAAAAACTGAACTGTCTGGATAAAGTCTGGCATAA
AGCATGCTTTCACTGTGAGACCTGCAAGGTGACCCTGAACATGAAGAACAACAAGAGTTATGAGAAGAAGTCTCACTGCA
ATGCACACTACCCCAAGCAGTCCTTCAACATGGTGGCCGAAACTCTGGAAATCCTTTGCTTCAAGCAACAGAATGAGCTA
CAGAGTCAGGTGTGCTACAAGGAGGAGAATAAGTGCAACGGTTATAGCCTGGTGGCAGACACGCCCGAGCTGTATAGCTG
CAGGGTATCAAGAAGACCCAGGATCAAATACCATGAGGAATTTGAGTAGAGCCACATAGGGCCCAGTGGAGGTGAAAGTG
TGGAATAGGGACACGGAGAATCCCAGACAGCAGCAGCTACCGAAGGCCCATAGAG
ORF - retro_rnor_946 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 67.09 % |
| Parental protein coverage: | 59.7 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MNPNCARCGKIVYPTEKVNCLDKFWHKACFHCETCKMTLNMKNYKGYEKKPYCNAHYPKQSFTMVADTPE |
| MN.NCA.C.K.VYP..K.NCLDK.WHKACFHCETCK.TLNMKN.K.YEKK..CNAHYPKQSF.MVA.T.E | |
| Retrocopy | MNHNCAWCSKTVYPM*KLNCLDKVWHKACFHCETCKVTLNMKNNKSYEKKSHCNAHYPKQSFNMVAETLE |
| Parental | NLRLKQQSELQSQVRYKEEFEKNKGKGFSVVADTPELQRIKKTQDQISNIKYHEEFEKSRMGPSGGEGIE |
| .L..KQQ.ELQSQV.YKEE...NK..G.S.VADTPEL............IKYHEEFE.S..GPSGGE..E | |
| Retrocopy | ILCFKQQNELQSQVCYKEE---NKCNGYSLVADTPELYSCRVSRR--PRIKYHEEFE*SHIGPSGGESVE |
| Parental | PERREAQ-DSSSYRRPTE |
| ....E.Q.DSSSYRRP.E | |
| Retrocopy | *GHGESQ<DSSSYRRPIE |
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 | 189 .45 RPM |
| SRP017611_kidney | 0 .00 RPM | 278 .50 RPM |
| SRP017611_liver | 0 .00 RPM | 118 .14 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_946 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_946 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_946 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 | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000038366 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000004132 | 1 retrocopy |
retro_rnor_946 ,
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