RetrogeneDB ID: | retro_mmus_774 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 11:27507627..27508022(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000082243 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Pdpn | ||
| Ensembl ID: | ENSMUSG00000028583 | ||
| Aliases: | Pdpn, Gp38, OTS-8, RANDAM-2, T1-alpha, T1a, T1alpha | ||
| Description: | podoplanin [Source:MGI Symbol;Acc:MGI:103098] |
Retrocopy-Parental alignment summary:
>retro_mmus_774
ATTGTGACCCCACGTATGGAAGACAAAAGAGCAACCACAGGTGCTATTGGAGGGCTGAAAGAATCTACTGGCAAGGCACC
TCTGGTACCAACATAGAACGAGGGTGGGACAAGCCTCCCATTGAGGTACTGCCAACCTCAGGAACCTCACACCATGATCA
CAAAGAACATGAGAGTACAACCTCTGTCAAAGTTGTGACTAGCCACTCTGTGGACAAGAAAACAAGTCACCCCAATAGAG
ATAACGCAGGTGATGAAACGCAGACCACAGATAAGAAAGATGGCTTGCTAGTATTCTCCCTGGTTGGAATCACAGTTGGC
GTACTGTTAGCCATTGGCTTCGTCAGAGGGATCATTATTGTGGTTATGAGGAAGATTTCTGGAAGGTTCTCACCC
ORF - retro_mmus_774 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.45 % |
| Parental protein coverage: | 76.74 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MVPPGIEDKITTTGATGGLNESTGKAPLVPTQRERGT-KPPLEELSTSATSDHDHREHESTTTVKVVTSH |
| .V.P..EDK..TTGA.GGL.ESTGKAPLVPT..E.GT.KPP.E.L.TS.TS.HDH.EHESTT.VKVVTSH | |
| Retrocopy | IVTPRMEDKRATTGAIGGLKESTGKAPLVPT*NEGGT<KPPIEVLPTSGTSHHDHKEHESTTSVKVVTSH |
| Parental | SVDKKTSHPNRDNAGDETQTTDKKDGLPVVTLVGIIVGVLLAIGFVGGIFIVVMKKISGRFSP |
| SVDKKTSHPNRDNAGDETQTTDKKDGL.V..LVGI.VGVLLAIGFV.GI.IVVM.KISGRFSP | |
| Retrocopy | SVDKKTSHPNRDNAGDETQTTDKKDGLLVFSLVGITVGVLLAIGFVRGIIIVVMRKISGRFSP |
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 | 9 .86 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 10 .81 RPM |
| SRP007412_heart | 0 .00 RPM | 5 .39 RPM |
| SRP007412_kidney | 0 .00 RPM | 5 .10 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .38 RPM |
| SRP007412_testis | 0 .00 RPM | 1 .37 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_774 was not detected
No EST(s) were mapped for retro_mmus_774 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_11740 | 887 libraries | 150 libraries | 35 libraries | 0 libraries | 0 libraries |
The graphical summary, for retro_mmus_774 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_774 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_774 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000007003 | 3 retrocopies | |
| Callithrix jacchus | ENSCJAG00000013772 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000028583 | 1 retrocopy |
retro_mmus_774 ,
|
| Pteropus vampyrus | ENSPVAG00000011180 | 1 retrocopy | |
| Tarsius syrichta | ENSTSYG00000005667 | 1 retrocopy |