RetrogeneDB ID: | retro_mmus_138 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 6:135309783..135310347(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000047104 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Pebp1 | ||
| Ensembl ID: | ENSMUSG00000032959 | ||
| Aliases: | Pebp1, HCNP, Pbp, Pbp1, Pbpr, Rkip | ||
| Description: | phosphatidylethanolamine binding protein 1 [Source:MGI Symbol;Acc:MGI:1344408] |
Retrocopy-Parental alignment summary:
>retro_mmus_138
ATGCCTACAGACATGAGCATGTGGACCGGGCCGCTGAGCCTCCACGAAGTGGATGAGCAGCCCCAGCACCTACTGCGGGT
CACCTACACCGAGGCGGAGGTGGAAGAGCTGGGCCAAGTGCTGACGCCCACCCAGGTTAAGCACAGACCCGGAAGCATTT
CATGGGATGGCCTTGACACAGGGAAACTCTACACCTTGATCCTCACAGACCCGGATGCTCCCAGTAGGAAGAAACCCGTG
TACAGGGAATGGCACCATTTTCTGGTGGTCAACATGAAAGGCAATGACATCAGCAGTGGGAACGTCCTCTCGGATTACGT
GGGTTCCGGACCTCCCAAGGGCACTGGCCTCCATCGCTATGTCTGGCTGGTGTACCAGCAGGACAAGCCACTGAGATGTG
ACGAACCCATCCTCACCAACCGGTCTGGAGACCATCGTGGGAAGTTCAAAACTGCAGCCTTCCGCAAGAAGTATCACCTG
GGAGCCCCGGTGGCCGGCACGTGTTACCAGGCAGAATGGGACAGCTATGTACCAAAGCTGTACAAACAGCTGTCTGGGAA
ATAG
ORF - retro_mmus_138 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.14 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAADISQWAGPLCLQEVDEPPQHALRVDYAGVTVDELGKVLTPTQVMNRPSSISWDGLDPGKLYTLVLTD |
| M..D.S.W.GPL.L.EVDE.PQH.LRV.Y....V.ELG.VLTPTQV..RP.SISWDGLD.GKLYTL.LTD | |
| Retrocopy | MPTDMSMWTGPLSLHEVDEQPQHLLRVTYTEAEVEELGQVLTPTQVKHRPGSISWDGLDTGKLYTLILTD |
| Parental | PDAPSRKDPKFREWHHFLVVNMKGNDISSGTVLSDYVGSGPPSGTGLHRYVWLVYEQEQPLSCDEPILSN |
| PDAPSRK.P..REWHHFLVVNMKGNDISSG.VLSDYVGSGPP.GTGLHRYVWLVY.Q..PL.CDEPIL.N | |
| Retrocopy | PDAPSRKKPVYREWHHFLVVNMKGNDISSGNVLSDYVGSGPPKGTGLHRYVWLVYQQDKPLRCDEPILTN |
| Parental | KSGDNRGKFKVETFRKKYNLGAPVAGTCYQAEWDDYVPKLYEQLSGK |
| .SGD.RGKFK...FRKKY.LGAPVAGTCYQAEWD.YVPKLY.QLSGK | |
| Retrocopy | RSGDHRGKFKTAAFRKKYHLGAPVAGTCYQAEWDSYVPKLYKQLSGK |
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 .07 RPM | 66 .21 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 54 .32 RPM |
| SRP007412_heart | 0 .00 RPM | 46 .63 RPM |
| SRP007412_kidney | 0 .02 RPM | 53 .36 RPM |
| SRP007412_liver | 0 .00 RPM | 45 .36 RPM |
| SRP007412_testis | 47 .29 RPM | 301 .74 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_138 was not detected
No EST(s) were mapped for retro_mmus_138 retrocopy.
| TSS No. | TSS Name | TSS expression level (Expr) in TPM range: | ||||
|---|---|---|---|---|---|---|
| no expression | 0 < Expr ≤ 1 | 1 < Expr ≤ 5 | 5 < Expr ≤ 10 | Expr > 10 | ||
| TSS #1 | TSS_119618 | 1063 libraries | 2 libraries | 1 library | 2 libraries | 4 libraries |
| TSS #2 | TSS_119619 | 1065 libraries | 2 libraries | 2 libraries | 0 libraries | 3 libraries |
The graphical summary, for retro_mmus_138 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)
retro_mmus_138 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_138 has 1 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Rattus norvegicus | retro_rnor_46 |