RetrogeneDB ID: | retro_mmus_2490 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 4:100567412..100568048(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000081553 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ccdc50 | ||
| Ensembl ID: | ENSMUSG00000038127 | ||
| Aliases: | Ccdc50, C3orf6 | ||
| Description: | coiled-coil domain containing 50 [Source:MGI Symbol;Acc:MGI:1914751] |
Retrocopy-Parental alignment summary:
>retro_mmus_2490
ATGGCCGACGTGAGTATAGATCAGTCCAAGATGCCGGGCGTGAAGGAAGTGTGTAGAGATTTTGCCGTCCTGGAGGACCA
CACCCTGGCCCATAGCCTGCAGGAACAGGAGATTGAGCATCATTTGGCATCCAACATTCAGCGGAACCGTCTGGTACAAC
ATGATCTACAGGTTGCTAAGCAGCTCCAAGAGGAAGACCTCACAGCCCAAACTCAGCTCCAGAAGCGCTACAAAGCCCTT
GAACAACATGATTGTGAAATTGCTCAGGAAATCCAGGAGAAGCTAACCATTGAGGCTGAGAGACGACGCATTCAGGAAAA
GAAGGATGAGGACATAGCACGTCTTTTGCAAGAGAAGGAACTATAGGAGGAGAAAAGGAGGAAGAAACACACTCCAGAGT
TTTCTGGGGGCAGTGCTTTTGGAGATAACTACTATTATGAGGATGGAGGAATGAAACCAAGAGGAATAAAAGAAGCTGTC
TCTACTCCAGCACAAGCGAGCTACAGAGACCAGGAATGGTATGATGCTGAAATTGCCCGGAAATTGCAAGAGGAAGAACT
TTTGGCTACTCATGTGGACATGAGAGCAGCTCAGGTTGCCCAGGATGAGGAAATTGCTCGACTTCTAATGGCTGAA
ORF - retro_mmus_2490 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 95.75 % |
| Parental protein coverage: | 80.3 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MADVSVDQSKLPGVKEVCRDFAVLEDHTLAHSLQEQEIEHHLASNIQRNRLVQHDLQVAKQLQEEDLKAQ |
| MADVS.DQSK.PGVKEVCRDFAVLEDHTLAHSLQEQEIEHHLASNIQRNRLVQHDLQVAKQLQEEDL.AQ | |
| Retrocopy | MADVSIDQSKMPGVKEVCRDFAVLEDHTLAHSLQEQEIEHHLASNIQRNRLVQHDLQVAKQLQEEDLTAQ |
| Parental | AQLQKRYKALEQHDCEIAQEIQEKLTIEAERRRIQEKKDEDIARLLQEKELQEEKRRKKHTPEFSGGSVF |
| .QLQKRYKALEQHDCEIAQEIQEKLTIEAERRRIQEKKDEDIARLLQEKEL.EEKRRKKHTPEFSGGS.F | |
| Retrocopy | TQLQKRYKALEQHDCEIAQEIQEKLTIEAERRRIQEKKDEDIARLLQEKEL*EEKRRKKHTPEFSGGSAF |
| Parental | GDNYYHEDGGMKPRGIKEAVSTPARASHRDQEWYDAEIARKLQEEELLATHVDMRAAQVAQDEEIARLLM |
| GDNYY.EDGGMKPRGIKEAVSTPA.AS.RDQEWYDAEIARKLQEEELLATHVDMRAAQVAQDEEIARLLM | |
| Retrocopy | GDNYYYEDGGMKPRGIKEAVSTPAQASYRDQEWYDAEIARKLQEEELLATHVDMRAAQVAQDEEIARLLM |
| Parental | AE |
| AE | |
| Retrocopy | AE |
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 .07 RPM | 64 .83 RPM |
| SRP007412_cerebellum | 0 .17 RPM | 68 .91 RPM |
| SRP007412_heart | 0 .09 RPM | 40 .34 RPM |
| SRP007412_kidney | 0 .27 RPM | 86 .22 RPM |
| SRP007412_liver | 0 .16 RPM | 54 .78 RPM |
| SRP007412_testis | 1 .23 RPM | 103 .60 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2490 was not detected
No EST(s) were mapped for retro_mmus_2490 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_98485 | 579 libraries | 412 libraries | 73 libraries | 5 libraries | 3 libraries |
The graphical summary, for retro_mmus_2490 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_2490 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2490 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000038127 | 1 retrocopy |
retro_mmus_2490 ,
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