RetrogeneDB ID: | retro_mmus_3449 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:48711868..48712535(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Habp4 | ||
| Ensembl ID: | ENSMUSG00000021476 | ||
| Aliases: | Habp4, 4933413D03Rik, 4933428J01Rik | ||
| Description: | hyaluronic acid binding protein 4 [Source:MGI Symbol;Acc:MGI:1891713] |
Retrocopy-Parental alignment summary:
>retro_mmus_3449
CTGAGAGGGCGTGGAGGCCCCAGAGGAGGTCTGAGGAACAGAGCTTTTGACTCCTTTGACCAAAGAGGGAAACGAGATTT
TAAAAGCTACAGTAGCAATGATAAAGCAAACAGAATGGAGGACAGTGTGGGTGGCTGTGGCATTTGCCTCTGGGCATCAG
GTGAAGACACTAGTGATACAGAGCCACCTGCACCCATGGAAGAGACCTGGATGGTGGAGGAGTGCCAGGGCGCCCTGGAC
GAGGAGTCTGCAGCCAAAATTCCTGAGCTGGAGGTAGAAGAGCAAAGTCAAGTCCAAGGGATGACCTTAGATGAGTGGAA
AACCTTCAAAAACAAGGCAGACCAAAGCCTGCCTTCAATATCCGGAAGCCGGAGTCCACAGTGCCGTCCAAGGCAGTGGT
GATTCCCAAGTCCGAATACAGAGACCATATGGAGAATGAGTATGAGGGTGGGTCTCCTGTCTTCCCGAAAGCTGGCAGTG
CTAGCACATCCCAGCTGGAGAGTAACTTTGGTAACCTTCCTCGCCTTGGTCGGGGAGCCAGAGGCAGCACCCGGGAAGGC
CGAGGAAGGATCAGAAGGAACAGAGAACTATGGCCCCCTGAGAAGAAGTGGTGACCCAAGATGTTGCTCCCAACCCGGAT
GACCCTGAGGACTTCCTCGCCCTGGCC
ORF - retro_mmus_3449 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.2 % |
| Parental protein coverage: | 53.64 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | LRSRG--RGGPGNRAFDSFDQRGKRDFERYSSNDKTNRMEDSMGGCGIRPWGSGKDTSDTEPPAPMEETS |
| LR.RG..RGG..NRAFDSFDQRGKRDF..YSSNDK.NRMEDS.GGCGI..W.SG.DTSDTEPPAPMEET. | |
| Retrocopy | LRGRGGPRGGLRNRAFDSFDQRGKRDFKSYSSNDKANRMEDSVGGCGICLWASGEDTSDTEPPAPMEETW |
| Parental | MMEECQGALDEESAAKVPELEVEEENQVQEMTLDEWK-NLQEQTRPKPEFNIRKPESTVPSKAVVIHKSR |
| M.EECQGALDEESAAK.PELEVEE..QVQ.MTLDEWK.NLQ.Q.RPKP.FNIRKPESTVPSKAVVI.KS. | |
| Retrocopy | MVEECQGALDEESAAKIPELEVEEQSQVQGMTLDEWK<NLQKQGRPKPAFNIRKPESTVPSKAVVIPKSE |
| Parental | YRDDMVKEDYEDESHVFRKAANDITSQLEINFGNLPRPGRGARGSTRGGRGRMRR-TENYGPR-AEVVTQ |
| YRD.M....YE..S.VF.KA....TSQLE.NFGNLPR.GRGARGSTR.GRGR.RR.TENYGP...EVVTQ | |
| Retrocopy | YRDHM-ENEYEGGSPVFPKAGSASTSQLESNFGNLPRLGRGARGSTREGRGRIRR>TENYGPL>EEVVTQ |
| Parental | DVAPNPDDPEDFPALA |
| DVAPNPDDPEDF.ALA | |
| Retrocopy | DVAPNPDDPEDFLALA |
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 .05 RPM | 159 .73 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 128 .27 RPM |
| SRP007412_heart | 0 .03 RPM | 60 .42 RPM |
| SRP007412_kidney | 0 .00 RPM | 56 .46 RPM |
| SRP007412_liver | 0 .03 RPM | 57 .92 RPM |
| SRP007412_testis | 0 .05 RPM | 350 .31 RPM |
RNA Polymerase II activity may be related with retro_mmus_3449 in 2 libraries
| ENCODE library ID | Target | ChIP-Seq Peak coordinates |
|---|---|---|
| ENCFF001YIJ | POLR2A | X:48711527..48711719 |
| ENCFF001YKA | POLR2A | X:48710725..48712195 |
No EST(s) were mapped for retro_mmus_3449 retrocopy.
No TSS is located nearby retro_mmus_3449 retrocopy 5' end.
retro_mmus_3449 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3449 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000021476 | 2 retrocopies |
retro_mmus_3449 , retro_mmus_613,
|