RetrogeneDB ID: | retro_mmus_2365 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 4:75380796..75381480(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000084026 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | 9630033F20Rik | ||
| Ensembl ID: | ENSMUSG00000038028 | ||
| Aliases: | 9630033F20Rik, AA793651, AI595337, C79710, C85509, Tigar | ||
| Description: | RIKEN cDNA 9630033F20 gene [Source:MGI Symbol;Acc:MGI:2442752] |
Retrocopy-Parental alignment summary:
>retro_mmus_2365
GCTGCCTCCGCTGGGTGGTTTCTGATCAAAGTGCAGTTTACACATGCTTTCTCCAGTGATCTCACAAGGACTAAGCAGAC
CATACATGGCATTTTGGAGAAAAGCAGATTTTGCAGAGACATAGCAGTGAAGTGTGACTCCCAGACTCCTGAAAGGATGT
ACGGGTTCACAGAAGGCAAACCGCTAAGCGAGCTTTGGACCGTGGCCAAAGCCGCTGGGGAAGTGTTCCATGTTCACCCC
ACCAGGAGGAGAGACAGTAGAGCAGGTAGAAATGCCTGGAAAGGATTTCTTTGATTTCATTTGCCAGCCAATCCTGGGCA
AGGCAGACCAGAGAGAAAGCTTCTTCCTTGGAGTGCCAGGCAGCTGTTTTGGAAGCTCTTTGGCAGAGATTTTCCTTTTT
GGGAAAACATGGCAGCTTTGGGCGAATCCCACAGGTGGCCCCTGGTTTTAGCAGGCAGCATCTTAGTTGTGAGCCATGGT
GTTTACATGCGAAGCCTCTTTGGTTATTTTCTGAGTGACCTCAGATGCTCATTGCCAGGCGCAAGAGACAAATTCGAACT
TTCCTCCATCATCCCCAGCACTGGCATCAGTGTCTTCGTCATAGTCTGCGAGTAAACATGCGAGCCATCAATTCAGTGGG
TTTGTATGAACCTCCAGGAGTATGTGAATGGAGTGACTTAAAAG
ORF - retro_mmus_2365 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.89 % |
| Parental protein coverage: | 85.13 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | AAAAGQFLSNVQFTHAFSSDLTRTKQTIHGILEKSRFCKDMAVKYDSRLRERMYGVAEGKPLSELRAMA- |
| AA.AG.FL..VQFTHAFSSDLTRTKQTIHGILEKSRFC.D.AVK.DS...ERMYG..EGKPLSEL...A. | |
| Retrocopy | AASAGWFLIKVQFTHAFSSDLTRTKQTIHGILEKSRFCRDIAVKCDSQTPERMYGFTEGKPLSELWTVA> |
| Parental | KAAGEECPMFTPPGGETVEQVKMRGKDFFDFICQLILGKAGQRESVLPGAPGSGLESSLAEVFPVGKHGS |
| K..G..C.MFTPPGGETVEQV.M.GKDFFDFICQ.ILGKA.QRES...G.PGS...SSLAE.F..GK... | |
| Retrocopy | KPLGK-CSMFTPPGGETVEQVEMPGKDFFDFICQPILGKADQRESFFLGVPGSCFGSSLAEIFLFGKTWQ |
| Parental | LGANPKGGT-LGLAASILVVSHGAYMRSLFGYFLSDLRCSLPGARDKLELSSITPNTGISVFIIDCEEAR |
| L.ANP.GG..L.LA.SILVVSHG.YMRSLFGYFLSDLRCSLPGARDK.ELSSI.P.TGISVF.I.CE... | |
| Retrocopy | LWANPTGGP<LVLAGSILVVSHGVYMRSLFGYFLSDLRCSLPGARDKFELSSIIPSTGISVFVIVCE*TC |
| Parental | QPSIQCVCMNLQEHLNGVTEK |
| .PSIQ.VCMNLQE..NGVT.K | |
| Retrocopy | EPSIQWVCMNLQEYVNGVT*K |
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 | 27 .19 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 24 .53 RPM |
| SRP007412_heart | 0 .00 RPM | 56 .25 RPM |
| SRP007412_kidney | 0 .00 RPM | 26 .01 RPM |
| SRP007412_liver | 0 .00 RPM | 13 .60 RPM |
| SRP007412_testis | 0 .00 RPM | 15 .55 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2365 was not detected
No EST(s) were mapped for retro_mmus_2365 retrocopy.
No TSS is located nearby retro_mmus_2365 retrocopy 5' end.
retro_mmus_2365 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2365 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000013237 | 2 retrocopies | |
| Mus musculus | ENSMUSG00000038028 | 1 retrocopy |
retro_mmus_2365 ,
|
| Tursiops truncatus | ENSTTRG00000016535 | 1 retrocopy |