RetrogeneDB ID: | retro_rnor_442 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 1:64369732..64370296(+) | ||
| 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: | ENSRNOG00000020013 | ||
| Aliases: | None | ||
| Description: | Proline/serine-rich coiled-coil protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q3KR66] |
Retrocopy-Parental alignment summary:
>retro_rnor_442
CCTACCTCCAACCAACCTGAGTTCCGGAGCAGTGATAAAAAGGGGTCAGCCAGAGCTGTTCTGGTGGCAGCTGGAAAGAA
GCCTCCAGCATAAAGAAGGAATCACCCACTTGCAATCTGTTCTCTGCATCCAAAATCCCAGGGCGCTCTCCTCTTGCAAA
CCGACTCTTCCACCTCGGAAGAAAACTGGGTCCGGCACACAGACAACAGCAAGCCTGCCAATCCCTGTCAGACCAGCTCC
ACAGGCCTCAGCTAGCAGTTCCCAGTGTTCACCCTCACTATAGGGAGCAGCCGCCAAGTGTTCTAGTCACCCATTCTCTC
AGCCATCCTCAAGCCTGTCACCCGAATGCCACTCACTGGGTGGGGTATACCACCTGGCAAAGGTGCCCTGGCTCCAGATC
CTCTCTCATCTCAGAAAGGGCAACCAAGTGCCATAGGGCACAGAGCTCCTGTTTCCCAGCAAACAAATCTTCCAACCACC
AGTGCTGGTTGAGGCAGGACCTCCAGTGCTGCTCCGGGCAGGATGCAGCCCCTCAGGAAAGCTGCAGTCCCTGGACCTAC
TAGA
ORF - retro_rnor_442 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 70.98 % |
| Parental protein coverage: | 57.75 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | PPSNLTGLRSSDKKGSARAGRVTAGKKP-SSIKKESPTCNLFSASKNPGRSPLA-QPTLPPRRKTGSGAR |
| P.SN....RSSDKKGSARA..V.AGKKP.SSIKKESPTCNLFSASK.PGRSPLA..PTLPPR.KTGSG.. | |
| Retrocopy | PTSNQPEFRSSDKKGSARAVLVAAGKKP<SSIKKESPTCNLFSASKIPGRSPLA<KPTLPPRKKTGSGTQ |
| Parental | TVASPPIPVRPAPQSSASNSQCSSWLQGAAAKSSSRLPFP-SAIPKPAIRMPLTGRSIPAGKGALAPDPL |
| T.AS.PIPVRPAPQ.SAS.SQCS..L.GAAAK.SS..PF..SAI.KP..RMPLTG..IP.GKGALAPDPL | |
| Retrocopy | TTASLPIPVRPAPQASASSSQCSPSL*GAAAKCSSH-PFS<SAILKPVTRMPLTGWGIPPGKGALAPDPL |
| Parental | PTQKGHPSTVGHRAPVSQRTNLPTIGAARGRTSSAARGRVQPLRKAAVPGPTR |
| ..QKG.PS..GHRAPVSQ.TNLP.................QPLRKAAVPGPTR | |
| Retrocopy | SSQKGQPSAIGHRAPVSQQTNLPXXXXXXXXXXXXXXXXXQPLRKAAVPGPTR |
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 |
|---|---|---|
| SRP017611_brain | 0 .29 RPM | 7 .19 RPM |
| SRP017611_kidney | 0 .70 RPM | 0 .42 RPM |
| SRP017611_liver | 0 .61 RPM | 0 .00 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_442 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_442 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_442 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 | |
| Rattus norvegicus | ENSRNOG00000020013 | 1 retrocopy |
retro_rnor_442 ,
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