RetrogeneDB ID: | retro_mmus_3461 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:61090998..61091704(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000083543 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Esrrb | ||
| Ensembl ID: | ENSMUSG00000021255 | ||
| Aliases: | Esrrb, Err2, Errb, Estrrb, Nr3b2 | ||
| Description: | estrogen related receptor, beta [Source:MGI Symbol;Acc:MGI:1346832] |
Retrocopy-Parental alignment summary:
>retro_mmus_3461
AAGTGTGACCGGGTATGTAGAGGCCAACAGAAGTACAAGGGATGGCTGGATTCAAAGAACAGCCCCTACCTGAGCCTACA
GATTTCCCCACCTGCTAAAAAGCCATCGACTAAGATTGTCTCATATCTACTGGTGGCTGAGCCAGACAAGTTTTATGTTA
TGCCTCCCAGTAATATACCTGAGGGAGATACCAAGGCCCTGGCTACTCTCTGTGTAGCCAGTTCACAAGCTTGTGGTCTT
TATTAGTTGGGCCAAGTACATCCCAGCCTTCTCCAGTCTGTCACCTGGGGACCAGATGAGTGCCTGGATGGAGATCCTCA
TCTTGGACATCATGTACCGCTTGCTGCCCTATGATGACAAACTGGCATATGCTGAGGACTGTATCATGGATAAGGAGCAC
ATGATGGGACTGCTGGAGCTTTACTGAGCTATCCTGCAACTGTTACACAGGTACAAGAAGCTCAAAGTAGAGAAGGAAGA
GTTTGGAATGCTCAAGGCCTTGGCCCTCACCAACTCAGATTCAGTGTACATTGAGGACCTGGAGGCTATGCAGAAGCTTC
AGGACCTGCTGCATGAGGCACTGCAGGACTATAAGCTGAGCCAACACCATGGGGAGCCATGGAGGACCAGCAAGCTGCTG
CTGATATTGCCCCTGCTGCCACAGACAGCAGCCAAAGTCTTGCAGCATTTCTACAGTGTAAAACTC
ORF - retro_mmus_3461 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.6 % |
| Parental protein coverage: | 53.3 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | RLDRVRGGRQKYKRRLDSENSPYLNLPISPPAKKPLTKIVSNLLGVEQDKLYAMPPNDIPEGDIKALTTL |
| ..DRV..G.QKYK..LDS.NSPYL.L.ISPPAKKP.TKIVS.LL..E.DK.Y.MPP..IPEGD.KAL.TL | |
| Retrocopy | KCDRVCRGQQKYKGWLDSKNSPYLSLQISPPAKKPSTKIVSYLLVAEPDKFYVMPPSNIPEGDTKALATL |
| Parental | CELADRE-LVFLINWAKHIPGFPSLTLGDQMSLLQSAWMEILILGIVYRSLPYDDKLAYAEDYIMDEEHS |
| C........VF.I.WAK.IP.F.SL..GDQMS....AWMEILIL.I.YR.LPYDDKLAYAED.IMD.EH. | |
| Retrocopy | CVASSQA>VVF-ISWAKYIPAFSSLSPGDQMS----AWMEILILDIMYRLLPYDDKLAYAEDCIMDKEH- |
| Parental | RLVGLLDLYRAILQLVRRYKKLKVEKEEFMILKALALANSDSMYIENLEAVQKLQDLLHEALQDYELSQR |
| ...GLL.LY.AILQL..RYKKLKVEKEEF..LKALAL.NSDS.YIE.LEA.QKLQDLLHEALQDY.LSQ. | |
| Retrocopy | -MMGLLELY*AILQLLHRYKKLKVEKEEFGMLKALALTNSDSVYIEDLEAMQKLQDLLHEALQDYKLSQH |
| Parental | HEEPRRAGKLLLTLPLLRQTAAKAVQHFYSVKL |
| H.EP.R..KLLL.LPLL.QTAAK..QHFYSVKL | |
| Retrocopy | HGEPWRTSKLLLILPLLPQTAAKVLQHFYSVKL |
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 | 2 .73 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 15 .41 RPM |
| SRP007412_heart | 0 .00 RPM | 26 .96 RPM |
| SRP007412_kidney | 0 .00 RPM | 45 .16 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .90 RPM |
| SRP007412_testis | 0 .00 RPM | 2 .84 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3461 was not detected
No EST(s) were mapped for retro_mmus_3461 retrocopy.
No TSS is located nearby retro_mmus_3461 retrocopy 5' end.
retro_mmus_3461 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3461 has 1 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Rattus norvegicus | retro_rnor_2876 |
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000020709 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000021255 | 1 retrocopy |
retro_mmus_3461 ,
|
| Rattus norvegicus | ENSRNOG00000010259 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000001302 | 1 retrocopy |