RetrogeneDB ID: | retro_mmus_2597 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 5:109236876..109238338(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000093543 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rad21 | ||
| Ensembl ID: | ENSMUSG00000022314 | ||
| Aliases: | Rad21, SCC1, mKIAA0078 | ||
| Description: | RAD21 homolog (S. pombe) [Source:MGI Symbol;Acc:MGI:108016] |
Retrocopy-Parental alignment summary:
>retro_mmus_2597
TATTGTAAATAAAAGATGGCTTTTCAGCCAAGTATTGTTGATTTACCTGAGGAAAATCCAGAAGTGGCTTATAATGTCAT
TATTTTCCCTAGGAATTTCAGAATTTTGAACAGCCATTACCAGACTTAGATGACACTGAGGTCACTCAGCAGTTTAGCCT
GAACCGGAGCGTAGTAGAAGAGATAACCATGAGAGAAGACATTGAACACATCAGTAACCTACAGGAAAATGATTTCAGTG
ACTTGGAATGGGCGACCATGAAATAATGAGAAAAGGCAGTGCTTTTGCATGTGAAGACATGTTAGTGAGCACCAGTGCTT
CTGACTTCCTCCTAGAGTCTGAACAGAGCACTAGCAAATTAAATGAAAAGATTAATTTTTAGAGTATGAAGACCAGTACA
AAGATGATAATTTTGGAGAAGGAAATGATGGCAGTATATTAGATGACAAACTTAGAATTAATAATGATGGTGGCATCCTT
GATGATCCCCCTGCCTTGTCTGAGGTCATGTTGCTAAAGCAGCCTGCACATGATGACATGGATGAAGATGACAATGGCTC
ATTGGGTGGGGCCTAACACTGTGAATCCTGTTGAACTGATGCCAACTATGACTGATCAGTCAAACTGGTCCCAACTGAGG
AAGAAGCATTTGCATTGGAGCTCATTGACATAACTGTCAAAGAAACAAAAATCAAGGGGAAGCTGATTGTTGAGGGTGTC
AAAGAATTGGATAGTAAGACAATTAGAGCCCAAATTAGTGATGATTCTGTTATTGTTACAACTATGGACCTGGCTCTGCC
TACCAAGAAGCTAATGCTGTGGAAAGAGAAGGGAGGAATGGAGAAGCTTTTCTCTGTACCAGCACAGCAATTAAGGAATA
ACTAACTACTGAAGCTCTTTACACACTACCTTACTCCACTTGTACCAGAAGACCTTAGGAAAATAAGGAAAGTAGGGAGA
GGGAGAAAATCTGGATGAGTTCCTCTAATAGTTTGAGAATCCAGGGGTTTCAAGAGAGGAGCAACAACCACAGCAGCAGC
AGCAGCCACCACAGGGACATGTCATTGATGAGCCCACTATAGAAGAGCCAAGCTACTTTCAGGAATCAGTGGTGGGGGCC
AGAAGAACAAAGATAGAAGAGTCAGCCATGCCCCCAACATCCCCTCAAGGATTTAAGCAAAAAGTCTGGCATGTAGACCC
AGAGCCTCTAATACCTCTTCAGCAGGCAGAACAAATGGAAATTCTACCAGCAGAATTTCCTCCAGAAGAGACTCTAAATA
TCTGTCAGCTGATAGCAGAATTAGAGCTTCTACCACAAAAGGAGAAGGATAAAGAAAAGGAGAAGGAAGAGGAAGAGTAT
AAAGATGCTTCAGGGGGTGATCAGGATCAAGAAGAAAGGAGATGGAACAAAAGGACTCAGCAGATGCTTCATGGTCTTCA
GCAAGCTCTTGCTAAAACTGGA
ORF - retro_mmus_2597 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.02 % |
| Parental protein coverage: | 78.43 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | FIKIKMAFRPGVVDLPEENREAAYNAITLPE-EFHDFDQPLPDLDDIDVAQQFSLNQSRVEEITMREEVG |
| ..K.KMAF.P..VDLPEEN.E.AYN.I..P..EF..F.QPLPDLDD..V.QQFSLN.S.VEEITMRE... | |
| Retrocopy | YCK*KMAFQPSIVDLPEENPEVAYNVIIFPR<EFQNFEQPLPDLDDTEVTQQFSLNRSVVEEITMREDIE |
| Parental | NISILQENDFGDF-GMDDREIMREGSAFEDDDMLVSTSASNLLLEPEQSTSNLNEKMNH-LEYEDQYKDD |
| .IS.LQENDF.D..GM.D.EIMR.GSAF...DMLVSTSAS..LLE.EQSTS.LNEK.N..LEYEDQYKDD | |
| Retrocopy | HISNLQENDFSDL<GMGDHEIMRKGSAFACEDMLVSTSASDFLLESEQSTSKLNEKINF<LEYEDQYKDD |
| Parental | NFGEGNDGGILDDKLISNNDGGIFDDPPALSEAGVMLPEQPAHDDMDEDDNGSLG-GPDSPDSVDPVEPM |
| NFGEGNDG.ILDDKL..NNDGGI.DDPPALSE..VML..QPAHDDMDEDDNGSLG.GP.....V.....M | |
| Retrocopy | NFGEGNDGSILDDKLRINNDGGILDDPPALSE--VMLLKQPAHDDMDEDDNGSLG>GPNTVNPVELMPTM |
| Parental | PTMTDQTT-LVPNEEEAFALEPIDITVKETKAKRKRKLIVDSVKELDSKTIRAQLSDYSDIVTTLDLAPP |
| ...TDQ...LVP.EEEAFALE.IDITVKETK...K.KLIV..VKELDSKTIRAQ.SD.S.IVTT.DLA.P | |
| Retrocopy | ---TDQSN<LVPTEEEAFALELIDITVKETKI--KGKLIVEGVKELDSKTIRAQISDDSVIVTTMDLALP |
| Parental | TKKLMMWKETGGVEKLFFLPAQPLWNNRLLKLFTRCLTPLVPEDLRKRRKG-GEADNLDEFLKEFENPEV |
| TKKLM.WKE.GG.EKLF..PAQ.L.NN.LLKLFT..LTPLVPEDLRK.RK..GE..NLDEFL..FENP.V | |
| Retrocopy | TKKLMLWKEKGGMEKLFSVPAQQLRNN*LLKLFTHYLTPLVPEDLRKIRKV>GEGENLDEFL**FENPGV |
| Parental | PREEQQPQQQQPQPQRDVIDEPIIEEPSRLQDSVMEASRTTIEESAMPPPPPQGVKRKAGQIDPEPSIPP |
| .REEQQPQQQQ..PQ..VIDEP.IEEPS..Q.SV..A.RT.IEESAMPP..PQG.K.K....DPEP.IP. | |
| Retrocopy | SREEQQPQQQQQPPQGHVIDEPTIEEPSYFQESVVGARRTKIEESAMPPTSPQGFKQKVWHVDPEPLIPL |
| Parental | QQVEQMEIPPVELPPEEPPNICQLIPELELLPEKEKEKEKEKEEEEEEEDEDASGGDQDQEERRWNKRTQ |
| QQ.EQMEI.P.E.PPEE..NICQLI.ELELLP.KEK.KEKEKEEEE.....DASGGDQDQEERRWNKRTQ | |
| Retrocopy | QQAEQMEILPAEFPPEETLNICQLIAELELLPQKEKDKEKEKEEEEY---KDASGGDQDQEERRWNKRTQ |
| Parental | QMLHGLQRALAKTG |
| QMLHGLQ.ALAKTG | |
| Retrocopy | QMLHGLQQALAKTG |
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 | 103 .59 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 142 .47 RPM |
| SRP007412_heart | 0 .00 RPM | 75 .55 RPM |
| SRP007412_kidney | 0 .00 RPM | 140 .75 RPM |
| SRP007412_liver | 0 .00 RPM | 49 .78 RPM |
| SRP007412_testis | 0 .00 RPM | 81 .19 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2597 was not detected
No EST(s) were mapped for retro_mmus_2597 retrocopy.
No TSS is located nearby retro_mmus_2597 retrocopy 5' end.
retro_mmus_2597 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2597 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000022314 | 1 retrocopy |
retro_mmus_2597 ,
|
| Nomascus leucogenys | ENSNLEG00000004817 | 1 retrocopy |