RetrogeneDB ID: | retro_mmus_376 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 1:153305431..153306475(+) | ||
| Located in intron of: | ENSMUSG00000026478 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000079138 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | 4930453N24Rik | ||
| Ensembl ID: | ENSMUSG00000059920 | ||
| Aliases: | 4930453N24Rik, AI649104 | ||
| Description: | RIKEN cDNA 4930453N24 gene [Source:MGI Symbol;Acc:MGI:1914859] |
Retrocopy-Parental alignment summary:
>retro_mmus_376
ATGTCGGGGCTCAGCCACTTAGAGTCGGAGGGCTGCCGAAACCTACTCGGCCTGCTGGACAACGACGAGATCATTGCCCT
TTGCGACACCATCACCAACCGCCTGGTGCAGCCTGTGGACCGCCAAGATGCTATTCATGCAATATTAGTGTATAGCCAAA
ATGTAGAAGAACTTCTGAGGCTCAAAAAAGTCCACCGAGAAGTCATACTTAAGTATTTGGCAAAGCAAGGGGTGGTTGTA
CCTCCAACTGCTGAAAAACACAATCTTATTCAGTATGCAAAAGATTACTGGGGAAAACAGTCACGAAAACTGAAGGACAC
AGCAGAGCCAGTTACAGAGACGGAGGACATCCAGCTCTTGGAGCAGCAGGCAAAGGAAGATAAAGCAGCTGAAAAGGTTG
ATTTTCGTCGCTTAGGAGAAGAATTCTGTCACTGGTTCTTTGAACTTCTTAATTCTCAGAATCCTTTTCTGGGCCCACCT
CAAAACGACTGGGGCCCACAGCCCTTCTGGCACGACGCCAAGCTTAGGTTTTATTATAACACCTCAGAACAAAACATGGT
AGACTACCAAGGAGCAGAAATCGTGAGCCTTCGCTTACTGTCATTAGCTAAAGAGGAATTTCTCTTTCTCAGTCCCAACC
TTGATTCTCAAGGACCAAAATGTGTGTCTTCTCCTCATGGATTAGTTATGGTTGGAGTTGCAGGGACTGTCCACCGAGGA
AATTCTTGTTTGGGCACATTTGAGCAAATTTTTGGACTTATCCGAAGCTCTTTTGTGGAAAATATTTGGAAAATCAAATT
TATCAACCTGAGAATCATTGGAGGAAGTTCCCTTACTCCTGAATCAGTACTGAAGCCATCTGTAACATTTAAACTGAGTG
ATCTGGAGGCCTTTTATAACGTAATCACTTTGTGTAATAGCCCTGAAGTAAGACCTAATGTAAGGCAGATAATAGATAGT
GGCACTGGAGACCAGGTTTTACATAGTGGAGATGAGGCATTGTTGAACAAAAGGGAAATGAATTTGCAAAACCCTCTAAA
GCAT
ORF - retro_mmus_376 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.82 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSGLSHLESEGCRNLLGLLDNDEIMALCDTVTNRLVQPVDRQDAIHAILVYSQNVEELLRRKKVHREVIF |
| MSGLSHLESEGCRNLLGLLDNDEI.ALCDT.TNRLVQPVDRQDAIHAILVYSQNVEELLR.KKVHREVI. | |
| Retrocopy | MSGLSHLESEGCRNLLGLLDNDEIIALCDTITNRLVQPVDRQDAIHAILVYSQNVEELLRLKKVHREVIL |
| Parental | KYLAKQGVVVPPTAEKHNLIQYAKDYWAKQSPKLKDTAEPVTKTEDIQLFKQQAKEDKEAEKVDFRRLGE |
| KYLAKQGVVVPPTAEKHNLIQYAKDYW.KQS.KLKDTAEPVT.TEDIQL..QQAKEDK.AEKVDFRRLGE | |
| Retrocopy | KYLAKQGVVVPPTAEKHNLIQYAKDYWGKQSRKLKDTAEPVTETEDIQLLEQQAKEDKAAEKVDFRRLGE |
| Parental | EFCHWFFELLNSQNPFLGPPQDDWGPQHFWHDAKLRFYYNTSEQNTTDYQGAEIVSLRLLSLVKEEFLFL |
| EFCHWFFELLNSQNPFLGPPQ.DWGPQ.FWHDAKLRFYYNTSEQN..DYQGAEIVSLRLLSL.KEEFLFL | |
| Retrocopy | EFCHWFFELLNSQNPFLGPPQNDWGPQPFWHDAKLRFYYNTSEQNMVDYQGAEIVSLRLLSLAKEEFLFL |
| Parental | SPNLDSQGLKCASSPHGLVMVGVAGTVHRGNSCLGIFEQIFGLIRSPFVENTWKIKFINLRIIGGSSLAP |
| SPNLDSQG.KC.SSPHGLVMVGVAGTVHRGNSCLG.FEQIFGLIRS.FVEN.WKIKFINLRIIGGSSL.P | |
| Retrocopy | SPNLDSQGPKCVSSPHGLVMVGVAGTVHRGNSCLGTFEQIFGLIRSSFVENIWKIKFINLRIIGGSSLTP |
| Parental | ESVLKPSVTFEPSDLEAFYNVITLCNSPEVRPNVRQIIDSGTGDQVLHSGDEALLNKREMNLLTPLKH |
| ESVLKPSVTF..SDLEAFYNVITLCNSPEVRPNVRQIIDSGTGDQVLHSGDEALLNKREMNL..PLKH | |
| Retrocopy | ESVLKPSVTFKLSDLEAFYNVITLCNSPEVRPNVRQIIDSGTGDQVLHSGDEALLNKREMNLQNPLKH |
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 .09 RPM | 16 .38 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 18 .11 RPM |
| SRP007412_heart | 0 .03 RPM | 14 .54 RPM |
| SRP007412_kidney | 0 .10 RPM | 18 .17 RPM |
| SRP007412_liver | 0 .11 RPM | 15 .70 RPM |
| SRP007412_testis | 2 .70 RPM | 354 .71 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_376 was not detected
No EST(s) were mapped for retro_mmus_376 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_70446 | 907 libraries | 98 libraries | 35 libraries | 15 libraries | 17 libraries |
The graphical summary, for retro_mmus_376 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_376 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_376 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000059920 | 3 retrocopies |
retro_mmus_2986, retro_mmus_376 , retro_mmus_695,
|
| Tursiops truncatus | ENSTTRG00000002941 | 1 retrocopy |