RetrogeneDB ID: | retro_rnor_2150 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 5:72304911..72305616(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Cnppd1 | ||
| Ensembl ID: | ENSRNOG00000018325 | ||
| Aliases: | Cnppd1, RGD735175 | ||
| Description: | Protein CNPPD1 [Source:UniProtKB/Swiss-Prot;Acc:Q6P7B2] |
Retrocopy-Parental alignment summary:
>retro_rnor_2150
CTCTACACTGATCCTCGGGAGATCTTTGAGGTGCTGAGTTGGCTGGAGAGTTGTGTGCCTGAGCAGCAAGGACGGCGGCG
GGGCTGGTACACCTACACAGACCTGTGTGTGCTGCTGGAGCAGCCAATGTGGCAGCTCTCTCTGGGCTCCCTCTGCCAGC
GGCTGGTAAAGCTGTCCTGCCTATTAGCCATGGCATATGTGAGCAGTGTGGCCCTGGCTGTGGCATTCGTGGCTGTAATA
CACTAGTCCTTGGGTCTGTCCTCCAGCCCCTCACCAAGTCCTCCTGAACTCACACTGGTCCCCAAGAACCTCTTGCAGCC
CTGCATACCTGCCCCTGTGCCACAGTGCCTGACTAATGTCTCCAGCTGCCTGGAAGACAGTGTAGAGTTGCCGTCGCTCT
GGGGCAGTCTTCTGGACCCATTGACACCCCCTCTGATGCCTCCTCCAGACCCTCCTGCCCCACCTACTCCTTTCCACAAA
TGCCCCTTTTGCCAGAAGTTCCAGAGAAACCCCCCAAATTGCCGTGCCTGTCACCAGCCTAACCGTACAGTGTCTATTGA
TCCTATCCACCCCTTTTACCATACCCATGGCCTGGCCCCACCCTGGGTCTGGAGCCCAGTGGCCCCTCCATTCCTCCAGC
CCCAGCAGTGTTCTCTTTTTAGTGTCATGAAGCTGGCTCGCCTCACGTCTGTTATTTTCCCAGGC
ORF - retro_rnor_2150 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.02 % |
| Parental protein coverage: | 57.6 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LYTDPREIFEVLSWLESCVAEQQGRRRGWYTYTDLCVLLEQPMWQLSLGSLCQRLVKLSCLLAVAYVSSV |
| LYTDPREIFEVLSWLESCV.EQQGRRRGWYTYTDLCVLLEQPMWQLSLGSLCQRLVKLSCLLA.AYVSSV | |
| Retrocopy | LYTDPREIFEVLSWLESCVPEQQGRRRGWYTYTDLCVLLEQPMWQLSLGSLCQRLVKLSCLLAMAYVSSV |
| Parental | ALAVASMAVIHQSLGLSSSPSPSPPELTLVPKNLLQPCIPAPVPQCLTNVSSCLEDSVELPSLWGSLLDP |
| ALAVA..AVIH.SLGLSSSPSPSPPELTLVPKNLLQPCIPAPVPQCLTNVSSCLEDSVELPSLWGSLLDP | |
| Retrocopy | ALAVAFVAVIH*SLGLSSSPSPSPPELTLVPKNLLQPCIPAPVPQCLTNVSSCLEDSVELPSLWGSLLDP |
| Parental | LTPPLMPPPDPPAPPTPFHKCPFCQKFQRNPPNCRACHQPNRTVSIGPIHPFYHTHGLAPPWLWSPVAPP |
| LTPPLMPPPDPPAPPTPFHKCPFCQKFQRNPPNCRACHQPNRTVSI.PIHPFYHTHGLAPPW.WSPVAPP | |
| Retrocopy | LTPPLMPPPDPPAPPTPFHKCPFCQKFQRNPPNCRACHQPNRTVSIDPIHPFYHTHGLAPPWVWSPVAPP |
| Parental | FLQPQQCSLFSVMKLARLTSVIFPG |
| FLQPQQCSLFSVMKLARLTSVIFPG | |
| Retrocopy | FLQPQQCSLFSVMKLARLTSVIFPG |
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 .72 RPM | 27 .46 RPM |
| SRP017611_kidney | 2 .79 RPM | 56 .52 RPM |
| SRP017611_liver | 2 .08 RPM | 28 .91 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2150 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2150 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2150 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000015328 | 1 retrocopy | |
| Pteropus vampyrus | ENSPVAG00000010786 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000018325 | 1 retrocopy |
retro_rnor_2150 ,
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