RetrogeneDB ID: | retro_mmus_1808 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 19:8272530..8274705(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Cast | ||
| Ensembl ID: | ENSMUSG00000021585 | ||
| Aliases: | None | ||
| Description: | calpastatin [Source:MGI Symbol;Acc:MGI:1098236] |
Retrocopy-Parental alignment summary:
>retro_mmus_1808
GGATCATCTTCTAAACCAGGAGAAAAAAAAGGATCCAAAGAGGTGACAGCTTCCTCTGCTGCCACCAGCAATTCTCCCAG
TATCAGTACCACAGAAGCTAAGACTGTGAAAACAGAGTCTGAGAAGTCACAATCAAGTGAGAAAGGAACAAAAGAGGTAA
AGTCAAGCAGAGGAGATTGCCTGCCACCTGTGGTTTATGAGAAAAAGTCAAAAGGATGGTCAAAGGAAGGGTCAGAGCCC
AAAAATCTTTCCAAGCACACATCAAATAAAGGAAGTAAGCATGCTCATAAAGAAAAAGCACTTTCCAGATCAAATGAACA
GATGGTGTCAGAGAAACCATCAGAATCAAAGACAAAATTTCAAGTGTTCCTTCTGCTGCTGGAGAGACTGTGGCTGGAGG
TGGGACTGTGGCCACTGCCTTGTACAACGTGGTTGGTAAGAAAAAAGAACATGAATCATTCACACCAGCTTTACCTATGC
ACTCCACACTGAGCAAGCCATCTGACAAGTCAGGCATGGATGCTGTCTTGGATGACCTGATATACACCTTAGGTGAACGT
GAAGATACTAACAAAGATGATCCACCATATACTGGACCAGTAGTTTTAGACCCAATGGATTCTACCTATCTTGAGGCATT
GGGTATAAAAGAAGGGACTATTCCTCCAGAGTATAGGAAACTTTTAGAAAAAGATGAAGGGATCACATGACCTCTTCCAG
ACTCTCTTAAACCTATGGAGTCTGACCATGCTATAGATGCCTTGTCATCTGATTTCACCTATAATTCTTCAACTGGAAAG
CAAAGTGAGAAAGAGAAGTCTACTGGGGAAATTTTCAAAGCTCAGTCTGTAGGAGTGACCAGAAGTTCTGTTCCCCCCGA
GGAGAAGAAAAGGAAAGTGGAAGAGGGGGTCATAAATGATCAAGCTCTTCAGGCTCTGTCAGATTCACTGGGCACCCAGC
AGCCACATCCTCAGAGCCACTTTAGCCAAGCTGAACAAGTCAAAGGGGCAAAAGCAAAAGAAGAAAGACAGGAGAAGTGT
GGTGAAGATGAGGACACAGCCCCAGCTGAGTACAGGTTAAAACCAGCAAAGGATAAAGATGGAAAACCGCTATTGCCAGA
GCCTGAAGAAACATCTACGTGCCTGAGTGAGTCAGTGCTGATTGGGGAGCTTTCAGCAGATTTTGGCTGATCTACATATC
AAGACAAACCATCTATGCCAGCTGAAAAGAAATCTAATGACACATCCCAAACTCCTCTGAGGGAGACTGTGCCTTGGGCC
TCCATGTGCAGTATACTGTCAGCACCACACAAACTAGAATCCTTGAAGGGCTTGGTGCCAGAAGATGCTGTTGAAGCCTT
GGCTAAAAGCCTGGGGACAAAGGAAGCAGATCCAGAATATGAAAAATCTGTGGAGGATAATGTCAAGGAGAAAGCTAAAG
AAGAAGAGCACGAAAAACTTGGTGGAAAAGAAGAAACGGTGCCTCCTGATTATTGACTAGAAGAAGTCAAGGATAAGGAT
GGAAAACCACTCCTGCCCAAAGAATCCCAGGAACAACTTGCACCCTTAAACGATGACTTCCTTCTTGATGTGTCATCTCA
GGACTTCTCCAGTCTGGCAAATATATCGTCTCTTGAATTTGAAGATGCCAAACTTTCTGCTGCCATTTCTGAAGTGTTTC
CCAGACACCTGCTCCAAGCACCCATGCAGCAGTCCCACTGCCTGGAACTGAGCAGAGAGATAAAGACTCGATGATGCCTT
GGTTGTACTTTTTGACAGTCTTGGATAAAGACAGCGTGATCTAGATGAGAAGAAACCACTAGATGATAAAGTGAAGGAAA
AAAGTCAAAGCAGAGAAAGCGAGAAACTGGGAGAAAGAGACGACACCATCCCCCCTGAATATAGGCATCTCTTGGATAAT
GATGGGAAGGACAAACCAGAGAAGCCACTGACTAAGAAAACAGAGAAACCTGATCAGGACCGGGACCCCATTGATGCCCT
CTCAGAAGATTTGGGTGGCTGCCCCTCAACTACAGAGACCTCAAAGAATACAGCAAAGGAGAAGAGCAAGAAGACTTCAA
CTTCCAAAGCATCCAAGGATAGAGAGAAAATAAAGGACTCTTCCAAGACAGAGGAAGTGTCCAAGACAAAGGCTAATGAA
GATGCAAGACACAGT
ORF - retro_mmus_1808 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.59 % |
| Parental protein coverage: | 96.42 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | GSDEKKAASLGSSQPSRPHVGEAATATKVTASSAATSKSPSMSTTETKAVKTESKKPQSSEQPVVHEKKS |
| GS..K.....GS.................T............S....K..K...........PVV.EKKS | |
| Retrocopy | GSSSKPGXXXGSKEVTASSAATSNSPSISTTEAKTVKTESEKSQSSEKGTKEVKSSRGDCLPPVVYEKKS |
| Parental | KGGPKEGSEPKNLPKHTSSTGSKHAHKEKALSRSNEQMVSEKPSESKTKFQ-DVPSAGGESVAGGGTVAT |
| KG..KEGSEPKNL.KHTS..GSKHAHKEKALSRSNEQMVSEKPSESKTKFQ..VPSA.GE.VAGGGTVAT | |
| Retrocopy | KGWSKEGSEPKNLSKHTSNKGSKHAHKEKALSRSNEQMVSEKPSESKTKFQ<SVPSAAGETVAGGGTVAT |
| Parental | ALDKVVGKKKEQKPFTPASPVQSTPSKPSDKSGMDAALDDLIDTLGGHEDTNRDDPPYTGPVVLDPMYST |
| AL..VVGKKKE...FTPA.P..ST.SKPSDKSGMDA.LDDLI.TLG..EDTN.DDPPYTGPVVLDPM.ST | |
| Retrocopy | ALYNVVGKKKEHESFTPALPMHSTLSKPSDKSGMDAVLDDLIYTLGEREDTNKDDPPYTGPVVLDPMDST |
| Parental | YLEALGIKEGTIPPEYRKLLEKNEGITQPLPDSPKPMGTDQAIDALSSDFTCSSPTGKQSEKEKSTGEIF |
| YLEALGIKEGTIPPEYRKLLEK.EGIT.PLPDS.KPM..D.AIDALSSDFT..S.TGKQSEKEKSTGEIF | |
| Retrocopy | YLEALGIKEGTIPPEYRKLLEKDEGIT*PLPDSLKPMESDHAIDALSSDFTYNSSTGKQSEKEKSTGEIF |
| Parental | KAQSAGVTRSSVPPKEKKRKVEEEVINDQALQALSDSLGTRQPDPPSHVSQAEQVKEAKAKEERQEKCGE |
| KAQS.GVTRSSVPP.EKKRKVEE.VINDQALQALSDSLGT.QP.P.SH.SQAEQVK.AKAKEERQEKCGE | |
| Retrocopy | KAQSVGVTRSSVPPEEKKRKVEEGVINDQALQALSDSLGTQQPHPQSHFSQAEQVKGAKAKEERQEKCGE |
| Parental | DEDTVPAEYRLKPAKDKDGKPLLPEPEETSKSLSESELIGELSADFDRSTYQDKPSTPAEKKSNDTSQTP |
| DEDT.PAEYRLKPAKDKDGKPLLPEPEETS..LSES.LIGELSADF..STYQDKPS.PAEKKSNDTSQTP | |
| Retrocopy | DEDTAPAEYRLKPAKDKDGKPLLPEPEETSTCLSESVLIGELSADFG*STYQDKPSMPAEKKSNDTSQTP |
| Parental | PGETVPRASMCSIRSAPPKLASLKGVVPEDAVETLAGSLGTREADPEHEKTVEDKVKEKAKEEEHEKLGE |
| ..ETVP.ASMCSI.SAP.KL.SLKG.VPEDAVE.LA.SLGT.EADPE.EK.VED.VKEKAKEEEHEKLG. | |
| Retrocopy | LRETVPWASMCSILSAPHKLESLKGLVPEDAVEALAKSLGTKEADPEYEKSVEDNVKEKAKEEEHEKLGG |
| Parental | KEETVPPDYRLEEVKDKDGKPLLPKESQEQLAPLSDDFLLDALSQDFSSPANISSLEFEDAKLSAAISEV |
| KEETVPPDY.LEEVKDKDGKPLLPKESQEQLAPL.DDFLLD..SQDFSS.ANISSLEFEDAKLSAAISEV | |
| Retrocopy | KEETVPPDY*LEEVKDKDGKPLLPKESQEQLAPLNDDFLLDVSSQDFSSLANISSLEFEDAKLSAAISEV |
| Parental | -VSQTPAPSTHAAAPLPGTEQKDKE-LDDALDELSDSLGQRPPDPDENKPLDDKVKEKIKPEHSEKLGER |
| .VSQTPAPSTHAA.PLPGTEQ.DK..LDDAL..L.DSLG.R..D.DE.KPLDDKVKEK.....SEKLGER | |
| Retrocopy | <VSQTPAPSTHAAVPLPGTEQRDKD<LDDALVVLFDSLG*RQRDLDEKKPLDDKVKEKSQSRESEKLGER |
| Parental | DDTIPPEYRHLLDNDGKDKPEKPPTKKTEKPDQDRDPIDALSEDLDSCPSTTETSKNTAKGKSKKTSSSK |
| DDTIPPEYRHLLDNDGKDKPEKP.TKKTEKPDQDRDPIDALSEDL..CPSTTETSKNTAK.KSKKTS.SK | |
| Retrocopy | DDTIPPEYRHLLDNDGKDKPEKPLTKKTEKPDQDRDPIDALSEDLGGCPSTTETSKNTAKEKSKKTSTSK |
| Parental | ASKDGEKTKDSSKKTEEVSKPKAKEDARHS |
| ASKD.EK.KDSS.KTEEVSK.KA.EDARHS | |
| Retrocopy | ASKDREKIKDSS-KTEEVSKTKANEDARHS |
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 .02 RPM | 8 .48 RPM |
| SRP007412_cerebellum | 0 .13 RPM | 14 .94 RPM |
| SRP007412_heart | 0 .03 RPM | 109 .33 RPM |
| SRP007412_kidney | 0 .08 RPM | 77 .83 RPM |
| SRP007412_liver | 0 .00 RPM | 39 .93 RPM |
| SRP007412_testis | 0 .18 RPM | 238 .48 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1808 was not detected
No EST(s) were mapped for retro_mmus_1808 retrocopy.
No TSS is located nearby retro_mmus_1808 retrocopy 5' end.
retro_mmus_1808 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1808 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000021585 | 2 retrocopies |
retro_mmus_1807, retro_mmus_1808 ,
|