RetrogeneDB ID: | retro_mmus_655 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 10:71980124..71980634(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000043859 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Hn1l | ||
| Ensembl ID: | ENSMUSG00000024165 | ||
| Aliases: | Hn1l, 2810430B18Rik, AL022629, C16orf34, D17Ertd441e | ||
| Description: | hematological and neurological expressed 1-like [Source:MGI Symbol;Acc:MGI:1196260] |
Retrocopy-Parental alignment summary:
>retro_mmus_655
ATGTTCCAGGGCATGGACAGCCACTCTGGCGGGTTGGGCTCCAGATCCATGAAGCCACCAGGAGGAGAATCGAGTGATCT
TTTTGGAAGTCTAGAAGAACGCCTTCCTTCAACACGCAAACCAAATAGGATGGCATCCAATATTTTTGGACCACCTGAAG
AGCCTAAAAATATACCCAAGAGGACAAATCCACCAGGGGGCAAAGGAAGTGGGATTTTTGATGAATCAACTCCTGTAAAA
ACTCGCCAACGTCTGAATCCACCCGGTGGGAAGACCAGTGACATATTTGGGTCCCCAATTACTGCCACTGCACCTCTGGC
ACACCCAAACAAGCCCAAGGATCATGTTTTGCTATGTGAAGGCGAAGACTCTAAATCCGACCTGAACGCAGCAACAAACG
CCACACCCAGGGGAGAGCATGCAAAGAAACCGGAGCTAACACCTACAGTTGACAATCATGAGCCCAGACTGGGGCCAAGA
CCTCGCTCCCACAACAAAGTTCTGAACCCA
ORF - retro_mmus_655 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.88 % |
| Parental protein coverage: | 88.95 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MFQGADSQAGKSGSRSMKPPGGESSDLFGSPEEGISSS-KPNRMASNIFGPTEEPKNIPKRTNPPGGKGS |
| MFQG.DS..G..GSRSMKPPGGESSDLFGS.EE...S..KPNRMASNIFGP.EEPKNIPKRTNPPGGKGS | |
| Retrocopy | MFQGMDSHSGGLGSRSMKPPGGESSDLFGSLEERLPSTRKPNRMASNIFGPPEEPKNIPKRTNPPGGKGS |
| Parental | GIFDESTPVQTRQRLNPPGGKTSDIFGSPVTATAPLAHPNKPKDHVLLCEGEDSKSDLKAATDSTPRGEQ |
| GIFDESTPV.TRQRLNPPGGKTSDIFGSP.TATAPLAHPNKPKDHVLLCEGEDSKSDL.AAT..TPRGE. | |
| Retrocopy | GIFDESTPVKTRQRLNPPGGKTSDIFGSPITATAPLAHPNKPKDHVLLCEGEDSKSDLNAATNATPRGEH |
| Parental | SDKGSSKEVEHAKIPEPTPTVDSHEPRLGP |
| ..K...........P...P...SH...L.P | |
| Retrocopy | AKKPELTPTVDNHEPRLGPRPRSHNKVLNP |
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 .02 RPM | 4 .49 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 4 .73 RPM |
| SRP007412_heart | 0 .00 RPM | 5 .32 RPM |
| SRP007412_kidney | 0 .00 RPM | 24 .00 RPM |
| SRP007412_liver | 0 .00 RPM | 18 .92 RPM |
| SRP007412_testis | 61 .79 RPM | 5 .21 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_655 was not detected
No EST(s) were mapped for retro_mmus_655 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_5068 | 1064 libraries | 2 libraries | 2 libraries | 1 library | 3 libraries |
| TSS #2 | TSS_5069 | 1063 libraries | 3 libraries | 0 libraries | 2 libraries | 4 libraries |
The graphical summary, for retro_mmus_655 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_655 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_655 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 11 parental genes, and 18 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ailuropoda melanoleuca | ENSAMEG00000008232 | 1 retrocopy | |
| Cavia porcellus | ENSCPOG00000005352 | 2 retrocopies | |
| Dipodomys ordii | ENSDORG00000007521 | 1 retrocopy | |
| Macropus eugenii | ENSMEUG00000008873 | 4 retrocopies | |
| Mus musculus | ENSMUSG00000024165 | 3 retrocopies |
retro_mmus_1204, retro_mmus_655 , retro_mmus_709,
|
| Oryctolagus cuniculus | ENSOCUG00000015551 | 1 retrocopy | |
| Pteropus vampyrus | ENSPVAG00000016673 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000024661 | 2 retrocopies | |
| Sorex araneus | ENSSARG00000012440 | 1 retrocopy | |
| Sarcophilus harrisii | ENSSHAG00000012700 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000011377 | 1 retrocopy |