RetrogeneDB ID: | retro_rnor_2955 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | X:96188645..96189021(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Egln1 | ||
| Ensembl ID: | ENSRNOG00000019773 | ||
| Aliases: | None | ||
| Description: | Egl nine homolog 1 [Source:UniProtKB/Swiss-Prot;Acc:P59722] |
Retrocopy-Parental alignment summary:
>retro_rnor_2955
GGGCAGTACCAAATCATGGTTGATTGTTACCCAGGCAATGAAACAGGCTATATCCATCATGTCAATAACCCAAATGGAAA
TGGAAGATGCAGGAATTGTACTTTTTATCTAAATAAAATTTGGGGTGCCAAGGTAAGTGGAGGTATCCTTCAAATTTTTC
CAGAAGGCAAAGCCCAGTTTGCTGTCATTAAACTCAAATTTGATAGACTGCTGTTTTTCTTGGCATAACCCTCATCAAGT
ACAGCCAGCATACACTACAAGGTATTCAGTAATTGTTTGCTATTTTGAAGCAGATGAGTGAGCAAAAACTAAAGTAAAAT
ATTTAATAGGTGAGAAAGGTGTGAGCATTGAACTCAAGCCACATTCAGTCAGCAAA
ORF - retro_rnor_2955 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 68.99 % |
| Parental protein coverage: | 57.66 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | GRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRL |
| G....MV.CYPGN.TGY..HV.NPNG.GRC..C..YLNK.W.AKVSGGIL.IFPEGKAQFA.I..KFDRL | |
| Retrocopy | GQYQIMVDCYPGNETGYIHHVNNPNGNGRCRNCTFYLNKIWGAKVSGGILQIFPEGKAQFAVIKLKFDRL |
| Parental | L-FFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYLTGEKGVRVELKPNSVSK |
| L.F.W....NPH.VQPAY.TRY...V.YF.ADE.A..KVKYL.GEKGV..ELKP.SVSK | |
| Retrocopy | L>FSW---HNPHQVQPAYTTRYSVIVCYFEADE*AKTKVKYLIGEKGVSIELKPHSVSK |
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 | 19 .20 RPM |
| SRP017611_kidney | 0 .00 RPM | 28 .05 RPM |
| SRP017611_liver | 0 .00 RPM | 6 .72 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2955 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2955 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2955 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 13 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Echinops telfairi | ENSETEG00000007202 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000019773 | 11 retrocopies |
retro_rnor_1086, retro_rnor_1783, retro_rnor_2109, retro_rnor_2110, retro_rnor_2411, retro_rnor_2885, retro_rnor_2938, retro_rnor_2939, retro_rnor_2955 , retro_rnor_507, retro_rnor_948,
|
| Ictidomys tridecemlineatus | ENSSTOG00000023570 | 1 retrocopy |