RetrogeneDB ID: | retro_mmus_3574 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:12619476..12620282(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000083199 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Nop56 | ||
| Ensembl ID: | ENSMUSG00000027405 | ||
| Aliases: | Nop56, 2310044F10Rik, Nol5a | ||
| Description: | NOP56 ribonucleoprotein [Source:MGI Symbol;Acc:MGI:1914384] |
Retrocopy-Parental alignment summary:
>retro_mmus_3574
TCCTGGTGTCTGAGTGATTCCCAAGGCCCAGCAAAAAGGGACCAAGTTTCCAGAGCCCTGAAGACAAGGGGTAACACACC
AAAATATGGACTCATTTTTCATTCCACCTTCATTGGCCGAGCAGCTGCAAAGAACAAAGGCCGTATCTCCCGATACCTAG
CAAACAAATGCAGTATTGCCTCGAGAATTGATTGCTTCTCTGAGGTCCCCACAAGTGTATTTGGGGAAAAACTCCGAGAA
CAAGTTGAGGAACGGCTGTCTTTCTATGAGACTGGAGAGATCCCACGGAAGAACCTGGATGTCATGAGAGAAGCCGTGGT
TCAGGCAGAGGAAGCGGCTGCTGAAATCACCAGAAAGCTGGAAAAACAGGAGAAGAAGCGCTTGAAGAAGGAAAAGAAGC
GACTGGCTGCACTGGCCCTGGCCACGTCAGAAAACAGAGTACCCCAGAGGAGTGTGAGGAGGTACATGAAAAACCTAAGA
AGAAGAAGAAGAAGAAGAAGTTAAAACCCCAGGAGACCCTACAGGAAAATGGAATGGAAGACCCACCTGTCTCTCTACCT
AAAACCAAGAAAAAGAAAGCTCCCAAGGAGGAGTTGGCCAGTGACCTTGAAGAGATGGCCACTAGCAGTGCTAAGAGAAA
GAAGTCCTTACCTAAGGAGGAAGTGGCCAGTGAACCAGAAGAGGAGGCAGCAAGCCCCACCACCCCTAAGAAGAAAAGGA
AATTTTCTGAGGAGCCTGAAGTTGCTGCTAACTTCACAAAGAGCAGCACAAAGAAAAAGAAAAAGTCCCAGAAAGCACAG
GAGGAT
ORF - retro_mmus_3574 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.63 % |
| Parental protein coverage: | 88.18 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | SWCLSDSQGPAKGDRVSRALKTRGNTPKYGLIFHSTFIGRAAAKNKGRISRYLANKCSIASRIDCFSEVP |
| SWCLSDSQGPAK.D.VSRALKTRGNTPKYGLIFHSTFIGRAAAKNKGRISRYLANKCSIASRIDCFSEVP | |
| Retrocopy | SWCLSDSQGPAKRDQVSRALKTRGNTPKYGLIFHSTFIGRAAAKNKGRISRYLANKCSIASRIDCFSEVP |
| Parental | TSVFGEKLREQVEERLSFYETGEIPRKNLDVMKEAVVQAEEAAAEITRKLEKQEKKRLKKEKKRLAALAL |
| TSVFGEKLREQVEERLSFYETGEIPRKNLDVM.EAVVQAEEAAAEITRKLEKQEKKRLKKEKKRLAALAL | |
| Retrocopy | TSVFGEKLREQVEERLSFYETGEIPRKNLDVMREAVVQAEEAAAEITRKLEKQEKKRLKKEKKRLAALAL |
| Parental | ASSEN-SSTP---EECEEVNEKSKKKKKLKP----QENGMEDPPVSLPKSKKKKAPKEELASDLEEMATS |
| A.SEN..STP...EE..E..........LKP....QENGMEDPPVSLPK.KKKKAPKEELASDLEEMATS | |
| Retrocopy | ATSEN<QSTPEECEEVHEKPXXXXXXXXLKPQETLQENGMEDPPVSLPKTKKKKAPKEELASDLEEMATS |
| Parental | SAKRKKSSPKEEVASEP-EEAASPTTPKKKRKFSEEPEVAANFTKSSTKKKKKSQKAQED |
| SAKRKKS.PKEEVASEP.EEAASPTTPKKKRKFSEEPEVAANFTKSSTKKKKKSQKAQED | |
| Retrocopy | SAKRKKSLPKEEVASEPEEEAASPTTPKKKRKFSEEPEVAANFTKSSTKKKKKSQKAQED |
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 |
|---|---|---|
| SRP007412_brain | 0 .05 RPM | 49 .37 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 47 .46 RPM |
| SRP007412_heart | 0 .00 RPM | 18 .15 RPM |
| SRP007412_kidney | 0 .00 RPM | 18 .17 RPM |
| SRP007412_liver | 0 .00 RPM | 19 .31 RPM |
| SRP007412_testis | 0 .00 RPM | 9 .33 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3574 was not detected
No EST(s) were mapped for retro_mmus_3574 retrocopy.
No TSS is located nearby retro_mmus_3574 retrocopy 5' end.
retro_mmus_3574 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3574 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000027405 | 4 retrocopies |