RetrogeneDB ID: | retro_mmus_2052 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 2:83353159..83353949(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000081400 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rps4x | ||
| Ensembl ID: | ENSMUSG00000031320 | ||
| Aliases: | Rps4x, Rps4, Rps4-1 | ||
| Description: | ribosomal protein S4, X-linked [Source:MGI Symbol;Acc:MGI:98158] |
Retrocopy-Parental alignment summary:
>retro_mmus_2052
ATGGCTCGTGGTCCCAAGAAACACCTGAAGTGTGTAGCTGCTCCAAAACATTAGATGCTGGATAAGTTGACTGGCGTGTT
TGCTCCTCGTCCATCCACTGGTCCTCACAAGCTGAGGGAATGCCCGCCTCTCATCATTTTCCTAAGGAACAGACTTAAGT
ATGCCCTGACTGGAGATGAAGTAAAAAAGATTTGCATGCAGCGATTCATTAAGATTGATGTGAAAGTCAGGACCGATATA
ACCTACCCTGCTGGGTTTATGGATGTCATCAGCATTGACAAGACCGGAGAGAACTTCCGTCTGATCTATGACACCAAGGG
TCGCTTTGCTGTTCATCGTATTACACCGGAGGAGGCCCAGTACAAGTTGTGCAAAGTGAGAAAGATCTTTGTGGGCACAA
AAGGAATCCCGCACCTGGTGACCCATGATGCTCGTACTATTCGGTACCCTGATCCCCTCATCAAGGTGAACGACACCATT
CAGATTGATTTGGAGACAGGCAAAATAACTGACTTCATCAAGTTCGACACTGGGAACCTGTGTATGGTGACTGGAGGTGC
TAACTTGGGAAAAATTGGTGTAATCACCAACAGAGAGAGACATCCCGGCTCTTTTTGATGTGGTTCATGTGAAAGATGCC
AATGGTAACAGCTTTGCCACTCGGCTGTCCAACATTTTTGTTATTGGCAATGGTAACAAACCATGGATCTCTCTTCCCAG
AGGAAAAGGAATCCGCCTCACTATTGCTGAAGAGAGAGACAAGAGGCTTGCGGCCAAACAGAGCAGTGGG
ORF - retro_mmus_2052 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.97 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFI |
| MARGPKKHLK.VAAPKH.MLDKLTGVFAPRPSTGPHKLREC.PLIIFLRNRLKYALTGDEVKKICMQRFI | |
| Retrocopy | MARGPKKHLKCVAAPKH*MLDKLTGVFAPRPSTGPHKLRECPPLIIFLRNRLKYALTGDEVKKICMQRFI |
| Parental | KIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHLV |
| KID.KVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEA.YKLCKVRKIFVGTKGIPHLV | |
| Retrocopy | KIDVKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAQYKLCKVRKIFVGTKGIPHLV |
| Parental | THDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRERHPGS-FDVVH |
| THDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLG.IGVITNRERHPGS.FDVVH | |
| Retrocopy | THDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGKIGVITNRERHPGS>FDVVH |
| Parental | VKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIRLTIAEERDKRLAAKQSSG |
| VKDANGNSFATRLSNIFVIG.GNKPWISLPRGKGIRLTIAEERDKRLAAKQSSG | |
| Retrocopy | VKDANGNSFATRLSNIFVIGNGNKPWISLPRGKGIRLTIAEERDKRLAAKQSSG |
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 .23 RPM | 93 .43 RPM |
| SRP007412_cerebellum | 1 .04 RPM | 46 .29 RPM |
| SRP007412_heart | 0 .12 RPM | 123 .84 RPM |
| SRP007412_kidney | 1 .12 RPM | 110 .38 RPM |
| SRP007412_liver | 1 .17 RPM | 108 .09 RPM |
| SRP007412_testis | 0 .23 RPM | 8 .42 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2052 was not detected
No EST(s) were mapped for retro_mmus_2052 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_89468 | 2 libraries | 0 libraries | 1 library | 7 libraries | 1062 libraries |
The graphical summary, for retro_mmus_2052 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_2052 was not experimentally validated.