RetrogeneDB ID: | retro_mmus_1971 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 2:129169500..129170482(+) | ||
| Located in intron of: | ENSMUSG00000084826 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000082274 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Setd3 | ||
| Ensembl ID: | ENSMUSG00000056770 | ||
| Aliases: | Setd3, 2610102I01Rik, 2610305M23Rik, 6030490B17Rik, D12Ertd771e | ||
| Description: | SET domain containing 3 [Source:MGI Symbol;Acc:MGI:1289184] |
Retrocopy-Parental alignment summary:
>retro_mmus_1971
TCCTTGGCTCTGATTCCTTTATGGGACATGTGCAATCCTACCAATGGCCTGATCACAACTGGCTATAACCTGGAAGATGA
CCGCTGTGAGTGTGTGGCTCTGCAGGACTTTCAGGCTGGAGATCAGATTTACATTTTTTATGGCACTCGGTCAAATGCAG
AGTTTGTGATCCACAGTGGTTTTTTTCTTTGACAATAATTCCCACGACAGAGTGAAAATTAAGCTGGGGGTGAATAAAAG
TGACAGGCTCTGCGCCATGAAGGCTGAGGTCCTGGCTCGGGCTGGCATCCCAACATCCAGTGTTTTTGCATTGCATTTTA
CTGAGCCACCCATCTCTGCCCAGCTTCTAGCTTTTCTCCGAGTATTCTGCATGACTGAAGAGGAGCTGAAAGAGCATTTG
CTAGGGGACAGCGCCATTGACAAGATCTTCACTCTGGGGAACGCAGAGTTTCCTGTCAGCTGGGACAATGAGGTCAAACT
TTGGACATTTCTGGAAGATAGAGCCTCACTTCTTTTAAAAACATATAAGACAACAATTGAGGAAGATAAGATCGTCTTGA
AAAATCCTGACCTCTCTGTCCGGGCCACAATGGCCATCAAATTGTGCTTGGGTGAAAAGGAGATTTTGGAAAAAGCAGTG
AAGAGTGCGGCCGCGAACTGGGAGTACTACCGTAAACACATGGAGGAGAGGGCACCACCGCAGAGATACGAGGAGAGTGA
CCTGGGGCTCTTGGAGGGTGGTGTGGGGGACTCAAGGCTCCCTCTGGTCCTGAGAAAGTTGGAGGAGGAGGCAGGTGTGC
AGGAGTCTCTGAGCCTCACAGAGACTGTCAGCAAAGTCAAGGCTGCTGAAAATGGGCTTGTCAATGGGGAAAACTTGATC
CCTAATGGGACCAGGTCTGAAAATGAAAGCTTAAGCCCAGAAGAAAGTGAAAACGTGACTGGAGAAGAGTCTTCAGGCAG
CATGGCCAAGGTGAAGGAGCGA
ORF - retro_mmus_1971 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.34 % |
| Parental protein coverage: | 55.05 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | TLALIPLWDMCNHTNGLITTGYNLEDDRCECVALQDFQAGDQIYIFYGTRSNAEFVIHSGFF-FDNNSHD |
| .LALIPLWDMCN.TNGLITTGYNLEDDRCECVALQDFQAGDQIYIFYGTRSNAEFVIHSGFF.FDNNSHD | |
| Retrocopy | SLALIPLWDMCNPTNGLITTGYNLEDDRCECVALQDFQAGDQIYIFYGTRSNAEFVIHSGFF>FDNNSHD |
| Parental | RVKIKLGVSKSDRLYAMKAEVLARAGIPTSSVFALHSTEPPISAQLLAFLRVFCMTEEELKEHLLGDSAI |
| RVKIKLGV.KSDRL.AMKAEVLARAGIPTSSVFALH.TEPPISAQLLAFLRVFCMTEEELKEHLLGDSAI | |
| Retrocopy | RVKIKLGVNKSDRLCAMKAEVLARAGIPTSSVFALHFTEPPISAQLLAFLRVFCMTEEELKEHLLGDSAI |
| Parental | DRIFTLGNAEFPVSWDNEVKLWTFLEDRASLLLKTYKTTIEEDKIVLKNPDLSVRATMAIKLRLGEKEIL |
| D.IFTLGNAEFPVSWDNEVKLWTFLEDRASLLLKTYKTTIEEDKIVLKNPDLSVRATMAIKL.LGEKEIL | |
| Retrocopy | DKIFTLGNAEFPVSWDNEVKLWTFLEDRASLLLKTYKTTIEEDKIVLKNPDLSVRATMAIKLCLGEKEIL |
| Parental | EKAVKSAAVNREYYRKHMEERAPLPRYEESDLGLLEGGVGDSRLPLVLRKLEEEAGVQESLSLTETVSKV |
| EKAVKSAA.N.EYYRKHMEERAP..RYEESDLGLLEGGVGDSRLPLVLRKLEEEAGVQESLSLTETVSKV | |
| Retrocopy | EKAVKSAAANWEYYRKHMEERAPPQRYEESDLGLLEGGVGDSRLPLVLRKLEEEAGVQESLSLTETVSKV |
| Parental | KAAENGLVNGENLIPNGTRSENESLSPEESENVTGEESSGSMAKVKER |
| KAAENGLVNGENLIPNGTRSENESLSPEESENVTGEESSGSMAKVKER | |
| Retrocopy | KAAENGLVNGENLIPNGTRSENESLSPEESENVTGEESSGSMAKVKER |
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 .14 RPM | 90 .34 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 85 .89 RPM |
| SRP007412_heart | 0 .09 RPM | 60 .86 RPM |
| SRP007412_kidney | 0 .06 RPM | 90 .97 RPM |
| SRP007412_liver | 0 .11 RPM | 66 .85 RPM |
| SRP007412_testis | 0 .27 RPM | 88 .05 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1971 was not detected
No EST(s) were mapped for retro_mmus_1971 retrocopy.
No TSS is located nearby retro_mmus_1971 retrocopy 5' end.
retro_mmus_1971 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1971 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000056770 | 2 retrocopies |
retro_mmus_1971 , retro_mmus_305,
|
| Ornithorhynchus anatinus | ENSOANG00000003153 | 1 retrocopy |