RetrogeneDB ID: | retro_mmus_2904 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 7:19911842..19912397(+) | ||
| Located in intron of: | ENSMUSG00000040511 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000089886 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rpl14 | ||
| Ensembl ID: | ENSMUSG00000025794 | ||
| Aliases: | Rpl14, 3100001N19Rik, AA407502, AL022816, CAG-ISL-7, CTG-B33, L14 | ||
| Description: | ribosomal protein L14 [Source:MGI Symbol;Acc:MGI:1914365] |
Retrocopy-Parental alignment summary:
>retro_mmus_2904
CGTTACGTGGAGGTTGGCCGGGTGGCCTACATTTCCTTTGGGCCCCATCCTGGAAAGCTGGTCGCAACTGTAGGTGTTAT
TGATCAAAAGAGGGTGTTAGTGGACGGACCCTGCACTCAGTGAGGAAACAGGCCACGCCTTTCAAATGCATGCAGCTCAC
TGGCTTCATCCTCGAGTTCCCGCACAGTGCCCACCAGAACTATGTACCAAAAGCTTGGGAGAAGGCAGGCATCGATGCGA
AGTGGGCAGCCACAAGATGGGCCAAGAAAATTGGTGCCAGAGAAAGGTTAGCCAAGATGACAGACTTTGATCATCTCAAA
GTCATGAAGGCAAAGAAAACGAGGAACCGAATAATCAAGACTGAAGTAGAGAAACTTCAAAGAGCTGCTATTCTGAAAGC
GGCTCACAAAAAGAGCAGCTGTTGCTCAGGCTGCCATTGTGGCAGCAGCAGCAGCAACTGCTACAGCTAACGTCCCAGCC
AAGAAGGCTACAGGACCAGGCAAGAAGCCCGCAGCCCAGAAAGCACCTGTTCCAAAGGCAGCTGGCAAGAAAGCG
ORF - retro_mmus_2904 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.32 % |
| Parental protein coverage: | 85.71 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | RYVEVGRVAYISFGPHAGKLVAIVDVIDQNRALVDGPCTR-VRRQAMPFKCMQLTDFILKFPHSARQKYV |
| RYVEVGRVAYISFGPH.GKLVA.V.VIDQ.R.LVDGPCT..VR.QA.PFKCMQLT.FIL.FPHSA.Q.YV | |
| Retrocopy | RYVEVGRVAYISFGPHPGKLVATVGVIDQKRVLVDGPCTQ<VRKQATPFKCMQLTGFILEFPHSAHQNYV |
| Parental | RKAWEKADINTKWAATRWAKKIDARERKAKMTDFDRFKVMKAKKMRNRIIKTEVKKLQRAAILKASPKK- |
| .KAWEKA.I..KWAATRWAKKI.ARER.AKMTDFD..KVMKAKK.RNRIIKTEV.KLQRAAILKA..KK. | |
| Retrocopy | PKAWEKAGIDAKWAATRWAKKIGARERLAKMTDFDHLKVMKAKKTRNRIIKTEVEKLQRAAILKAAHKK> |
| Parental | AAVAKAAIAAAAAAAAAKAKVPAKKATGPGKKAAGQKAPAQKAAGQKA |
| AAVA.AAI.AAAAA.A..A.VPAKKATGPGKK.A.QKAP..KAAG.KA | |
| Retrocopy | AAVAQAAIVAAAAATAT-ANVPAKKATGPGKKPAAQKAPVPKAAGKKA |
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 .33 RPM | 77 .31 RPM |
| SRP007412_cerebellum | 0 .26 RPM | 57 .84 RPM |
| SRP007412_heart | 0 .62 RPM | 77 .27 RPM |
| SRP007412_kidney | 0 .40 RPM | 91 .22 RPM |
| SRP007412_liver | 0 .19 RPM | 78 .51 RPM |
| SRP007412_testis | 0 .09 RPM | 31 .74 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2904 was not detected
No EST(s) were mapped for retro_mmus_2904 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_132223 | 17 libraries | 3 libraries | 205 libraries | 323 libraries | 524 libraries |
The graphical summary, for retro_mmus_2904 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_2904 was not experimentally validated.