RetrogeneDB ID: | retro_rnor_1676 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 2:210759155..210759514(-) | ||
| Located in intron of: | ENSRNOG00000050322 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Nip7 | ||
| Ensembl ID: | ENSRNOG00000020391 | ||
| Aliases: | Nip7, CGI-37, Nip7p, pEachy | ||
| Description: | 60S ribosome subunit biogenesis protein NIP7 homolog [Source:UniProtKB/Swiss-Prot;Acc:Q9WV50] |
Retrocopy-Parental alignment summary:
>retro_rnor_1676
AATAAGCTAGTGTCCCTGGGGATGAGTTTTAGAAAGTTTACTAAAACCCACAAGTTCTGGTTGTATGTTACAATTCTGGA
TTACCTTGCACCTTATGGCAAGTATAAAGTATGGATAAAGCCTGGAGCAGAGCAATCCTTCTTGTATGGCAACCATGTGT
TGGAAACCAGTCTGGGTCAATTCAATGAATATCCATCTCAGTACCAGGGAGTAGTGGTTTACTCCATGGCAGATGTTCCT
TTGGGTTTTAGGGTGCCAACAAATCTACCCAAGACTGCAGAAAAGTGCAACCCATGGTACTTGTCATGTTCCATCAAGCA
GACATTGGAGAGTACATATGCAACAAAAAGACATTGACT
ORF - retro_rnor_1676 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.86 % |
| Parental protein coverage: | 66.67 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | DKLVSLGTCFGKFTKTHKFRLHVTALDFLAPYAKYKVWIKPGAEQSFLYGNHVLKSGLGRITENTSQYQG |
| .KLVSLG..F.KFTKTHKF.L.VT.LD.LAPY.KYKVWIKPGAEQSFLYGNHVL...LG...E..SQYQG | |
| Retrocopy | NKLVSLGMSFRKFTKTHKFWLYVTILDYLAPYGKYKVWIKPGAEQSFLYGNHVLETSLGQFNEYPSQYQG |
| Parental | VVVYSMADVPLGFGV-AAKSTQDCRKVDPMAIVVFHQADIGEYIRHEETLT |
| VVVYSMADVPLGF.V.A.KSTQDCRKV.PM..V.FHQADIGEYI....TLT | |
| Retrocopy | VVVYSMADVPLGFRV<ANKSTQDCRKVQPMVLVMFHQADIGEYICNKKTLT |
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 | 7 .33 RPM |
| SRP017611_kidney | 0 .00 RPM | 10 .61 RPM |
| SRP017611_liver | 0 .00 RPM | 5 .72 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_1676 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_1676 was not experimentally validated.