RetrogeneDB ID: | retro_mmus_3672 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:98513902..98514306(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000081397 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Dctd | ||
| Ensembl ID: | ENSMUSG00000031562 | ||
| Aliases: | Dctd, 6030466N05Rik | ||
| Description: | dCMP deaminase [Source:MGI Symbol;Acc:MGI:2444529] |
Retrocopy-Parental alignment summary:
>retro_mmus_3672
AATACAGAAAACAACATTCTTGGGATTCGATACGATGGAATGTGAAAGGGGTTCAGTGACAACTTATTGTCTTGGAGAAC
AGCAGAAAATAGCTGACTACTAAATATCTTTATGTGTGCCATGCCAAGCTGAACACCATTGGGAACAAGAATTCAGCTGA
TATGAAGGGCTGCAATATGATCACTGCTTTGATCTCACGTAATGAACATGCTGAGTTCATCATCCAGGAAGGTATACAAG
AAGTTATTTTCATGTCAGATAAATACCATGACAGTGAACAGACAATGGGCATTAGGCTCGTGATTAAATTGCCTGGGGTT
ACATTCAGAAAATTCACACTGAAATGGAGCAAGATCGTCATTGACTTTGATTTAATTAATAGCCGACTGAGTCAGAAGCC
CCAG
ORF - retro_mmus_3672 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 70.8 % |
| Parental protein coverage: | 73.91 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | NTENKIVGIGYNGMPNGCSDDLLPWRRTAENK-LDTKYPYVCHAELNAIMNKNSADVKGCSMYVALFPCN |
| NTEN.I.GI.Y.GM..G.SD.LL.WR.TAEN..L.TKY.YVCHA.LN.I.NKNSAD.KGC.M..AL...N | |
| Retrocopy | NTENNILGIRYDGM*KGFSDNLLSWR-TAENS<LTTKYLYVCHAKLNTIGNKNSADMKGCNMITALISRN |
| Parental | ECAKLIIQAGIKEVIFMSDKYHDSEETTAARLLFKLAGVTFRKFTPKYSKIVIDFDSINSRPSQKPQ |
| E.A..IIQ.GI.EVIFMSDKYHDSE.T...RL..KL.GVTFRKFT.K.SKIVIDFD.INSR.SQKPQ | |
| Retrocopy | EHAEFIIQEGIQEVIFMSDKYHDSEQTMGIRLVIKLPGVTFRKFTLKWSKIVIDFDLINSRLSQKPQ |
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 | 7 .15 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 4 .08 RPM |
| SRP007412_heart | 0 .00 RPM | 1 .46 RPM |
| SRP007412_kidney | 0 .00 RPM | 1 .23 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .08 RPM |
| SRP007412_testis | 0 .00 RPM | 1 .51 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3672 was not detected
No EST(s) were mapped for retro_mmus_3672 retrocopy.
No TSS is located nearby retro_mmus_3672 retrocopy 5' end.
retro_mmus_3672 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3672 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000017516 | 3 retrocopies | |
| Mus musculus | ENSMUSG00000031562 | 1 retrocopy |
retro_mmus_3672 ,
|
| Rattus norvegicus | ENSRNOG00000013215 | 1 retrocopy | |
| Sarcophilus harrisii | ENSSHAG00000015218 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000001460 | 1 retrocopy |