RetrogeneDB ID: | retro_ptro_3012 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | GL391667.1:108355..108955(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PSRC1 | ||
| Ensembl ID: | ENSPTRG00000001045 | ||
| Aliases: | None | ||
| Description: | proline/serine-rich coiled-coil 1 [Source:HGNC Symbol;Acc:24472] |
Retrocopy-Parental alignment summary:
>retro_ptro_3012
ATGGAGGATTTGGAGGAAGATATAAGGTTTATTGTGGATGAGATCTTGGACTTTGGGGGGCTGTCACCATCTGACAGCCG
TGAGGAGGAAGACATAACAGTGTTGGTGACTCCAGAGAAACCATTTCGACAGGGCCTCTCCCACCGAAGTGACCCAAATG
CAGTGGCACCTGCCCCCCAGGGTGTGAGGCTCAGCCTAGGCCCCCTCAGCCCAGAGAAGCTGGAGGAGATCCTCGATGAG
GCCAACCGGCTGGCCGCTCAGCTGGAGCAGTGTGCCCTGCAGGATCGGGAGAGTGCAGGCGAGGGCCTGGGGCCTCGCCG
AGTGAAGCCCAGTCCTCGGCGGGAGACCTTTGTGCTGAAGGACAGTCCTGTCCGAGACCTGCTGCCCACTGTGAACTCTT
TGACGCGGAGCACCCCCTCCCCAAGCAGCCTGACGCCTCGACTCCGGAGCAATGATAGGAAGGGGTCGGTCAGGGCTCTC
CGGGCTACATCTGGAAAGAGGCCCTCCAACATGAAGAGGGAGTCACCCAATTGCAATCTGTTCCCTGCATCCAAAAGCCC
AGCATCTTCTCCTCTTACCCGATTGACTCCCCCAGTCCGG
ORF - retro_ptro_3012 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.0 % |
| Parental protein coverage: | 60.06 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MEDLEEDVRFIVDETLDFGGLSPSDSREEEDITVLVTPEKPLRRGLSHRSDPNAVAPAPQGVRLSLGPLS |
| MEDLEED.RFIVDE.LDFGGLSPSDSREEEDITVLVTPEKP.R.GLSHRSDPNAVAPAPQGVRLSLGPLS | |
| Retrocopy | MEDLEEDIRFIVDEILDFGGLSPSDSREEEDITVLVTPEKPFRQGLSHRSDPNAVAPAPQGVRLSLGPLS |
| Parental | PEKLEEILDEANRLAAQLEQCALQDRESAGEGLGPRRVKPSPRRETFVLKDSPVRDLLPTVNSLTRSTPS |
| PEKLEEILDEANRLAAQLEQCALQDRESAGEGLGPRRVKPSPRRETFVLKDSPVRDLLPTVNSLTRSTPS | |
| Retrocopy | PEKLEEILDEANRLAAQLEQCALQDRESAGEGLGPRRVKPSPRRETFVLKDSPVRDLLPTVNSLTRSTPS |
| Parental | PSSLTPRLRSNDRKGSVRALRATSGKRPSNMKRESPTCNLFPASKSPASSPLTRSTPPVR |
| PSSLTPRLRSNDRKGSVRALRATSGKRPSNMKRESP.CNLFPASKSPASSPLTR.TPPVR | |
| Retrocopy | PSSLTPRLRSNDRKGSVRALRATSGKRPSNMKRESPNCNLFPASKSPASSPLTRLTPPVR |
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_prefrontal_cortex | 0 .07 RPM | 35 .44 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 4 .66 RPM |
| SRP007412_heart | 0 .09 RPM | 0 .41 RPM |
| SRP007412_kidney | 3 .37 RPM | 1 .18 RPM |
| SRP007412_liver | 1 .57 RPM | 0 .98 RPM |
| SRP007412_testis | 0 .11 RPM | 3 .79 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_3012 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_3012 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_3012 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Pan troglodytes | ENSPTRG00000001045 | 1 retrocopy |
retro_ptro_3012 ,
|
| Rattus norvegicus | ENSRNOG00000020013 | 1 retrocopy |