RetrogeneDB ID: | retro_mmus_867 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 12:60526517..60527803(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Sgol1 | ||
| Ensembl ID: | ENSMUSG00000023940 | ||
| Aliases: | Sgol1, 3300001M08Rik, C81037, Sgo1 | ||
| Description: | shugoshin-like 1 (S. pombe) [Source:MGI Symbol;Acc:MGI:1919665] |
Retrocopy-Parental alignment summary:
>retro_mmus_867
ATGGCTAAGGAAAGGTGTCAGAAAAGGTCCTTTCAAGATACTCTTGAAGACATTAAGAAGCAAATGAAAGAAAAAAGAAA
TAAAAACTTGGCAGGGATTGGGAAATGCAAGTCCTTTATTGTTGCACCGAGCCAAGTACGCACTAGCACTGCTACACTAC
TGAAATATTACCAAGATAACAACAGGTTTAGTTTTGGCTTTGGAAAATGAAAAATCCAAAGTGAGAGAAGCACAGGATAT
CATCCTACAAGTGACAAGAGAATTCTACTACCTTACATGTCAGCTGTATACATTGAAAGAGAAGCTAACTTCCTGACAAT
GTGAAGAAACTACTGATAACTGGAAAGGACGTCCCTCAGAAGTGGTCTCCAGCATTGACAATATGACCAGGGTCTTGTCT
GTAATGACCTTACATCAAATTGCTCCTGAAGAAACTGATTGTCTCCACCAAACCTCAGCACCAAGTCCTGCTGTTACTCC
AGAAACACGGGGTTGCAATTTTGATTCAGGTAAAGACGAGTCTACTGATGAAGTCTTACCTGGAACTGTATCTGTCCATC
GCCACTTAAGGAAAGATTTTAGTAATGTAACTCACTCCACTACTTTGGAGGATTGTAAAGCCTGTCCAAGAGTGGCACAG
TCTCTGGAAGTTCAAAGATGTAGATGTAGAGAAGTAACCCTAACCCTGCATAGAATTGAAAATATAGAACAAAATGTTTG
TCTGTGGAACAAAGACCTAATTAACTTAGGCTCTAGACTGATTAACCCAGCAAAGATTACTAAAACACAAGAAGCCATTT
TATATTCATTTTCGCATCTAAACCTGAACAAGCATAAACGTGCACAAAAAAAGCAGAGCAGAGCAAAGAAAAACCAACCA
GAGATGCAAATCAAAATCCTCATTGAGGAGTAAGGGCAACAAAGGCAAAGATAAGCAGGGTTTACCCCCTACTACACAGG
ACAGAAGTATTGGTTCCAGTAATGCTTATGATTCTAATCTAAAAGAGACTATTCACCACACCCCTTCCCGACAAAAAAAA
ATGAGCAATGGCTGCAACAAAGAAACCAACAGCAGCAACTTAGAAGTGAGTGCCCTTGAATGTAGTACCTCTGAGGATGA
GTCTAACGACCTCTACCTGCCTCCTTAAAAGCGCTTGCGAGACTACACAGAGTCACACAGACCAGGTACCAGGACTCAGT
CTAAAAGAGGACCTAAGTACCCAGCTGAAAAATGGATGGAGGAGGTGCTGCCATCTACAGCTTCTACTGGTACCCCACCT
GAGACT
ORF - retro_mmus_867 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 72.62 % |
| Parental protein coverage: | 81.82 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MAKERCQKRSFQDTLEDIKNRMKEKRNKNLAGIGKRKSFIVAPGQVPTNTATLLRYYQDNNRL-LVLALE |
| MAKERCQKRSFQDTLEDIK..........LAGIGK.KSFIVAP.QV.T.TATLL..Y...N...LVLALE | |
| Retrocopy | MAKERCQKRSFQDTLEDIKKXXXXXXXXXLAGIGKCKSFIVAPSQVRTSTATLLK-YYQDNNR>LVLALE |
| Parental | NEKSKVREAQDVILQLRKECYYLTCQLYALKEKLTSRQSEETTQNWKGRPSDVVSSIDNTTRDLSGKSLQ |
| NEKSKVREAQD.ILQ...E.YYLTCQLY.LKEKLTS.Q.EETT.NWKGRPS.VVSSIDN.TR.LS...L. | |
| Retrocopy | NEKSKVREAQDIILQVTREFYYLTCQLYTLKEKLTS*QCEETTDNWKGRPSEVVSSIDNMTRVLSVMTLH |
| Parental | QIAVEETDCPYQTTEPSPAVTPETQGCDFDSGKVESTDEVLPRTISIRRHLRKDFSNISHSTTLEDCKAS |
| QIA.EETDC..QT..PSPAVTPET.GC.FDSGK.ESTDEVLP.T.S..RHLRKDFSN..HSTTLEDCKA. | |
| Retrocopy | QIAPEETDCLHQTSAPSPAVTPETRGCNFDSGKDESTDEVLPGTVSVHRHLRKDFSNVTHSTTLEDCKAC |
| Parental | PRVAQSLEVKGSRCREVTVTLHRLENV----CLWNKDQISLCSRLINPAKITET-EVILSSKPEQIESKH |
| PRVAQSLEV...RCREVT.TLHR.EN.....CLWNKD.I.L.SRLINPAKIT.T.E.IL.S.......KH | |
| Retrocopy | PRVAQSLEVQRCRCREVTLTLHRIENIEQNVCLWNKDLINLGSRLINPAKITKTQEAILYSFSHLNLNKH |
| Parental | KRARKR-RAEQRRTKQRCKSKSSLRSKGNKNKDKQGLPPTTLDGGIGSCDAYDFNLKGTVHPTPFR-QKM |
| KRA.K..RAEQR.T.QRCKSKSSLRSKGNK.KDKQGLPPTT.D..IGS..AYD.NLK.T.H.TP.R.... | |
| Retrocopy | KRAQKK>RAEQRKTNQRCKSKSSLRSKGNKGKDKQGLPPTTQDRSIGSSNAYDSNLKETIHHTPSRXXXX |
| Parental | NNGCNKETDSSNSEVSDLECSTSEDESDDLYLPPSKRLRDYRESERAVTRPRSKRGLQYPDGKERKEVLP |
| .NGCNKET.SSN.EVS.LECSTSEDES.DLYLPP.KRLRDY.ES.R..TR..SKRG..YP..K...EVLP | |
| Retrocopy | SNGCNKETNSSNLEVSALECSTSEDESNDLYLPP*KRLRDYTESHRPGTRTQSKRGPKYPAEKWMEEVLP |
| Parental | STAPTGIPPET |
| STA.TG.PPET | |
| Retrocopy | STASTGTPPET |
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 | 0 .14 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 0 .74 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .25 RPM |
| SRP007412_kidney | 0 .00 RPM | 0 .46 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .27 RPM |
| SRP007412_testis | 0 .00 RPM | 1 .33 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_867 was not detected
No EST(s) were mapped for retro_mmus_867 retrocopy.
No TSS is located nearby retro_mmus_867 retrocopy 5' end.
retro_mmus_867 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_867 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000013948 | 1 retrocopy | |
| Dasypus novemcinctus | ENSDNOG00000008694 | 1 retrocopy | |
| Equus caballus | ENSECAG00000012475 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000023940 | 2 retrocopies |
retro_mmus_3486, retro_mmus_867 ,
|
| Rattus norvegicus | ENSRNOG00000022499 | 1 retrocopy |