RetrogeneDB ID: | retro_mmus_3654 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:84018248..84018897(-) | ||
| Located in intron of: | ENSMUSG00000045103 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Psmf1 | ||
| Ensembl ID: | ENSMUSG00000032869 | ||
| Aliases: | Psmf1, AW048666, BC012260, PI31 | ||
| Description: | proteasome (prosome, macropain) inhibitor subunit 1 [Source:MGI Symbol;Acc:MGI:1346072] |
Retrocopy-Parental alignment summary:
>retro_mmus_3654
ATGGTGGCCTTGGAAGTTCTCTTTGCATCAGCCATTCTGACCATGAGCTGCCCTCAGGACTTCCTCATCTGTTTCCTGCA
CTATGAAGTGGTGCCAAAGGCTAATATTGCTTGGGCACCAGCGAGCAGCCAAATCCCAGTAGTAAGTGAGAATGACTGCT
AGCAACATGGAAGAGCAATATAAGAACTGTCCTCCAGTATGAATCTAAGGATGGAGCCAGGAAAATACTTTTTGAAAGCT
GTCTCTGTGGAGAATGGCATGATCATCAATGTGCTGGAACATGATACACAGAAGGGGCCAGATTAGATTCCTAACCTAGA
TGATTATACTAATGTATAAGATCAAAGTAATTTCCACAGGATCTATAAGAACAGTGAAGAGATTCAGTCTTGGATTAGAT
CTGAAATTATCACACCTACCTGAGAGCATAGGAGAAGGCTCTTATAAGCAATGTCCATCTGGAGGTCCTATCAGCCACCA
TCAGAGAGGTAAACCCACTCAAGAATGCCTCACACCATTCTCATACTAACCAGCAGCCCTTTTGGTGTGGTCCACTGAAT
CCATTTGCTGTCTTGAGAAGATCTAGACCCCCTATTGGTGTCAGCGAGTTGGAATAATTATGGATCCCCTGAGATTTTTG
CTTCCCAAA
ORF - retro_mmus_3654 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 58.3 % |
| Parental protein coverage: | 80.81 % |
| Number of stop codons detected: | 6 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | MAGLEVLFASAAPSMSCPQDALVCFLHWEVV-TNGYYALGTGDQPGPSDKKSELLPAKWNSNKELYALRY |
| M..LEVLFASA...MSCPQD.L.CFLH.EVV...G.Y.LGT..QP.PS.K...LL.A.W.SN.....L.Y | |
| Retrocopy | MVALEVLFASAILTMSCPQDFLICFLHYEVV<AKG*YCLGTSEQPNPSSK*E*LL-ATWKSNIRT-VLQY |
| Parental | ESKDGARKLL-LKAVSVENGMIINVLELGTQQVADLTLNLDDYIDAEDLSDFHRTYKNSEELRSQIRSGI |
| ESKDGARK.L.LKAVSVENGMIINVLE..TQ...D...NLDDY....D.S.FHR.YKNSEE..S.IRS.I | |
| Retrocopy | ESKDGARKIL>LKAVSVENGMIINVLEHDTQKGPD*IPNLDDYTNV*DQSNFHRIYKNSEEIQSWIRSEI |
| Parental | ITPIHEQW-EKARANSPPREFPPATAREVDPLQISSHRPHTSRQPAWRDPLSPFAVGGDDLDPFG-CQRG |
| ITP..E...EKA.......E...AT.REV.PL...SH..HT..QP.W..PL.PFAV......P.G.CQR. | |
| Retrocopy | ITPT*EHR<EKALISNVHLEVLSATIREVNPLKNASHHSHTNQQPFWCGPLNPFAVLRRSRPPIG<CQRV |
| Parental | GMIVDPLRSGFPR |
| G.I.DPLR...P. | |
| Retrocopy | GIIMDPLRFLLPK |
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 .00 RPM | 27 .73 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 27 .49 RPM |
| SRP007412_heart | 0 .03 RPM | 15 .81 RPM |
| SRP007412_kidney | 0 .00 RPM | 22 .93 RPM |
| SRP007412_liver | 0 .00 RPM | 25 .51 RPM |
| SRP007412_testis | 0 .00 RPM | 319 .53 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3654 was not detected
No EST(s) were mapped for retro_mmus_3654 retrocopy.
No TSS is located nearby retro_mmus_3654 retrocopy 5' end.
retro_mmus_3654 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3654 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000032869 | 1 retrocopy |
retro_mmus_3654 ,
|