RetrogeneDB ID: | retro_mmus_1888 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 2:15127604..15128593(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000083860 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ppid | ||
| Ensembl ID: | ENSMUSG00000027804 | ||
| Aliases: | Ppid, 4930564J03Rik, CYP-40, Ppidl, Ppif | ||
| Description: | peptidylprolyl isomerase D (cyclophilin D) [Source:MGI Symbol;Acc:MGI:1914988] |
Retrocopy-Parental alignment summary:
>retro_mmus_1888
CCACGCATCCCCGGCAGCCAAGCCCTCCAACTCCAAGTCTTCTTTGACGGGGACATCGGTGGGGAGCGAGTTGGACTAAT
TGTTTTAGAATTGTTTGCAGATATTGTTCCCAAAACTGCAGAAAATTTTCATGCATTGTACAGGAGAAAAAGGAACTGGG
TCCACTACCGGAAAGCCTCTCCATTTTAAAGGATGCCCTTTCTACCGAATTATTAAGAACTTTGTGATTCAGGGTGGAGA
CTTCTCAAATCAGAATGGGACAGGTGGCAAAAGTATTTATGGTGAAAAATTTGAAGATGAAATTTTTCATTATAAGCATG
ATCGGGAGGGTTTGCTGAGCATGGCAAATGCAGGTCCCAAATACGAGTGGTTCTCAGCTCTTTAACACAACAGTTCCAAC
TCCTCATTTGGATGGGAAACATGTGGTATTTGGTGAAGTCATAAAAGGACTAGGTTGGCAAGGATGCTTGAAATGTAGAA
GTGAATGGTGAAAAACCTGCCAAACTCTGTGTTATTGCAGAATGTGAAGAATTGAAAGAAGGGGACGACTGGGGAATATT
TCCCAAAGATGGCTCTGGTGACAGTCATCCAGACTTCCTGAGGATGCAGATATAGATTTAAAAGATGTAGATAAAATTTT
ATTAATATCTGAGGACTTAAAAAACATTAGAAATACTCTTTTCAAATCTCAGAACTGGGAGATGTCTATTAAACAATATG
TGAAGATTTTAAGTTATGTGGATAGTTCAAAGGCTGTTATTGAGAAAGCAGATAGATCCAGACTGCAACCTATAGCCTTA
AGTTGTGTACTGAATATTGGTGCTTGTAAGCTGAAGATGTCAAATTGGCAGGGGGCAATTGACAGTTGCTTAGAGGCTCT
TGAAATGGACCCTTCAAATACTAAAGCACTGTACTGAAAAGCGCAAGGATGGCTAGGATTGAAAGAGTTTGATCAAGCAT
TGGCTGATCTTAAGAAGGCACAGGAGATA
ORF - retro_mmus_1888 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.31 % |
| Parental protein coverage: | 89.46 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | PAAKPSNSKNPRVFFDVDIGGERVGRIVLELFADIV-PKTAENFRALCTGEKGTGSTTGKPLHFKGCPFH |
| P....S......VFFD.DIGGERVG.IVLELFADIV.PK....F...CTGEKGTGSTTGKPLHFKGCPF. | |
| Retrocopy | PRIPGSQALQLQVFFDGDIGGERVGLIVLELFADIV>PKLQKIFMH-CTGEKGTGSTTGKPLHFKGCPFY |
| Parental | RIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDREGLLSMANAGP-NTNGSQFFITTVPTPHLD |
| RIIK.F.IQGGDFSNQNGTGG.SIYGEKFEDE.FHYKHDREGLLSMANAGP.NT.GSQ.F.TTVPTPHLD | |
| Retrocopy | RIIKNFVIQGGDFSNQNGTGGKSIYGEKFEDEIFHYKHDREGLLSMANAGP>NTSGSQLFNTTVPTPHLD |
| Parental | GKHVVFGQVIKGLG-VARTLE-NVEVNGEKPAKLCVIAECGELKEGDDWGIFPKDGSGDSHPDF-PEDAD |
| GKHVVFG.VIKGLG..AR.LE.NVEVNGEKPAKLCVIAEC.ELKEGDDWGIFPKDGSGDSHPDF.PEDAD | |
| Retrocopy | GKHVVFGEVIKGLG<LARMLE<NVEVNGEKPAKLCVIAECEELKEGDDWGIFPKDGSGDSHPDF<PEDAD |
| Parental | IDLKDVDKILLISEDLKNIGNTFFKSQNWEMAIKKYAKVLRYVDSSKAVIEKADRSRLQPIALSCVLNIG |
| IDLKDVDKILLISEDLKNI.NT.FKSQNWEM.IK.Y.K.L.YVDSSKAVIEKADRSRLQPIALSCVLNIG | |
| Retrocopy | IDLKDVDKILLISEDLKNIRNTLFKSQNWEMSIKQYVKILSYVDSSKAVIEKADRSRLQPIALSCVLNIG |
| Parental | ACKLKMSNWQGAIDSCLEALEMDPSNTKALYRKAQGWQGLKEYDQALADLKKAQEI |
| ACKLKMSNWQGAIDSCLEALEMDPSNTKALY.KAQGW.GLKE.DQALADLKKAQEI | |
| Retrocopy | ACKLKMSNWQGAIDSCLEALEMDPSNTKALY*KAQGWLGLKEFDQALADLKKAQEI |
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 | 49 .39 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 41 .21 RPM |
| SRP007412_heart | 0 .00 RPM | 28 .61 RPM |
| SRP007412_kidney | 0 .02 RPM | 30 .09 RPM |
| SRP007412_liver | 0 .03 RPM | 28 .67 RPM |
| SRP007412_testis | 0 .05 RPM | 29 .59 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1888 was not detected
No EST(s) were mapped for retro_mmus_1888 retrocopy.
No TSS is located nearby retro_mmus_1888 retrocopy 5' end.
retro_mmus_1888 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1888 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 11 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Echinops telfairi | ENSETEG00000012655 | 2 retrocopies | |
| Macaca mulatta | ENSMMUG00000017768 | 2 retrocopies | |
| Mus musculus | ENSMUSG00000027804 | 6 retrocopies |
retro_mmus_1086, retro_mmus_1888 , retro_mmus_2228, retro_mmus_2555, retro_mmus_3254, retro_mmus_616,
|
| Rattus norvegicus | ENSRNOG00000027408 | 1 retrocopy |