RetrogeneDB ID: | retro_mmus_3038 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 7:73685506..73686506(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Snip1 | ||
| Ensembl ID: | ENSMUSG00000050213 | ||
| Aliases: | Snip1, 2410133M08Rik | ||
| Description: | Smad nuclear interacting protein 1 [Source:MGI Symbol;Acc:MGI:2156003] |
Retrocopy-Parental alignment summary:
>retro_mmus_3038
CTGAGCCCCGAACCCAGCGCTCCAGCCGCTAGCCTGCCCACCGCCAAGCCCAATGCTAGTCGGTCCCCAGACAAAAAGAA
AAGGAAGTCCTCCGGGAGAAGAAGCAAGTCCCCTCCAACTAAGAGAAGCCGGAGTCCCCACTACTCCACGGTCAAAGTGA
AGCAGGAACGTGAGGACCATCCACTGAGAGGACGAGAGGATCCACAACCCCGGGAGCCATCAGAACAGGAGCACAGGAGA
GCAAGGAACAGTGATGAGCAAGCCCCGCACCGGGGCCATTCCCACCAAAGGAGGAGCTCTGATGAGAGGCCTGTCAGTGG
ACAGGGCCGGGATAGAGACAGCCAGAACCTGAAGGCTCAGGAAGAAGAGAGGGACTTTCATAATGCCAGGCGCCAGGAGC
ATCGCCAGCAGAATGGAAGTGCTGGCAGCGGTGAGGTTCAAGAAGAGGTGATCCCTCACCCTGCTGGTAACAGAAGCAAA
GAGGTGCCCGTTAAAGAAAAACCATGCTTTGAACTTTCTGGGGCACTTCTTGAGGACACTAATACCTTCCGGGGTGTGGT
TATTAAATACAACGAGCCCCCAGAAGCCCGGATCCCCAAAAAACGGTGGCGTCTCTACCCCTTTAAAAATGATGAGCTGC
TTCCAGTCTTGTACATCCATCGACAAAGTGCATACCTTCTGGGTAGACATCGACGCATCGCAGACATTCCCATTGACCAT
CCCTCTTGCTCAAAGCAACATGCTGTCTTGCAGTACCGGCTTGTGGAGTCCACCCGTGCTGATGGCACGGTTGGTCGGAG
TGTGAAGCCCTTCATCATTGATCTCTGCTCAGCCAACGGAACATTCTTAAACAACAAGCGTATTGAGCCACAGAGATACT
ATGAACTGAAAGAAAGCGATGTACTTAAATTTGGATTCAGTAGCCGAGATTACGTCTTGCTTCATGAGTCTTCAGACACC
TCTGAACTTGAAGAAGGAAGATGAGGGGGAGGAGGAGGAA
ORF - retro_mmus_3038 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.74 % |
| Parental protein coverage: | 85.64 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LSPPAAEPGHS--GHRGSRARSPAKKKSKSSGRRSKSPRTKRSQSPHYPMVKVKQEREDHPRRGREDRQH |
| LSP....P..S.........RSP.KKK.KSSGRRSKSP.TKRS.SPHY..VKVKQEREDHP.RGRED.Q. | |
| Retrocopy | LSPEPSAPAASLPTAKPNASRSPDKKKRKSSGRRSKSPPTKRSRSPHYSTVKVKQEREDHPLRGREDPQP |
| Parental | REPSEQEHRRARNS-ERDRHRGHSRQGRSSDERPVSGQDRDRDSQNLQAQEEERDFHNARRREHRQQNES |
| REPSEQEHRRARNS.E...HRGHS.Q.RSSDERPVSGQ.RDRDSQNL.AQEEERDFHNARR.EHRQQN.S | |
| Retrocopy | REPSEQEHRRARNSDEQAPHRGHSHQRRSSDERPVSGQGRDRDSQNLKAQEEERDFHNARRQEHRQQNGS |
| Parental | AGSEA--QEVIPRPAGNRSKEVPVKEKPSFELSGALLEDTNTFRGVVIKYSEPPEARIPKKRWRLYPFKN |
| AGS.....EVIP.PAGNRSKEVPVKEKP.FELSGALLEDTNTFRGVVIKY.EPPEARIPKKRWRLYPFKN | |
| Retrocopy | AGSGEVQEEVIPHPAGNRSKEVPVKEKPCFELSGALLEDTNTFRGVVIKYNEPPEARIPKKRWRLYPFKN |
| Parental | DEVLPVMYIHRQSAYLLGRHRRIADIPIDHPSCSKQHAVFQYRLVEYTRADGTVGRRVKPYIIDLGSGNG |
| DE.LPV.YIHRQSAYLLGRHRRIADIPIDHPSCSKQHAV.QYRLVE.TRADGTVGR.VKP.IIDL.S.NG | |
| Retrocopy | DELLPVLYIHRQSAYLLGRHRRIADIPIDHPSCSKQHAVLQYRLVESTRADGTVGRSVKPFIIDLCSANG |
| Parental | TFLNNKRIEPQRYYELKEKDVLKFGFSSREYVLLHESSDTSELD-RKEDEDDEE |
| TFLNNKRIEPQRYYELKE.DVLKFGFSSR.YVLLHESSDTSEL.........EE | |
| Retrocopy | TFLNNKRIEPQRYYELKESDVLKFGFSSRDYVLLHESSDTSELE>KEDEGEEEE |
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 | 10 .21 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 10 .73 RPM |
| SRP007412_heart | 0 .00 RPM | 8 .00 RPM |
| SRP007412_kidney | 0 .00 RPM | 9 .49 RPM |
| SRP007412_liver | 0 .00 RPM | 10 .73 RPM |
| SRP007412_testis | 0 .00 RPM | 30 .19 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3038 was not detected
No EST(s) were mapped for retro_mmus_3038 retrocopy.
| TSS No. | TSS Name | TSS expression level (Expr) in TPM range: | ||||
|---|---|---|---|---|---|---|
| no expression | 0 < Expr ≤ 1 | 1 < Expr ≤ 5 | 5 < Expr ≤ 10 | Expr > 10 | ||
| TSS #1 | TSS_136969 | 1031 libraries | 25 libraries | 13 libraries | 2 libraries | 1 library |
The graphical summary, for retro_mmus_3038 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)
retro_mmus_3038 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3038 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000001963 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000017132 | 2 retrocopies | |
| Mus musculus | ENSMUSG00000050213 | 2 retrocopies |
retro_mmus_3038 , retro_mmus_941,
|
| Otolemur garnettii | ENSOGAG00000008634 | 2 retrocopies |