RetrogeneDB ID: | retro_mmus_3708 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:146599753..146600982(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000081718 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Zzz3 | ||
| Ensembl ID: | ENSMUSG00000039068 | ||
| Aliases: | Zzz3, 3110065C23Rik, 6430567E01Rik, AA408566, AI481057, AW556059, R75514 | ||
| Description: | zinc finger, ZZ domain containing 3 [Source:MGI Symbol;Acc:MGI:1920453] |
Retrocopy-Parental alignment summary:
>retro_mmus_3708
ATGATAGATCTTTGGTTGTACAGTTATCAGAGACTGCTACAGACCATTGCTGCTCTTGAGGCTCAGTGTTCTCAAGCAGT
ACAAGACCTGGAAAGTTTAGGCAAACATGAGAGAGAAGCACTAAAAAATCCTATTGGATTTGTGGAGAAACTTCAGAAGA
AGGCTGACATAGGGCTTCCATACCCACAGAGAGTTGTTCAGTTACCTGAGATCATGTGGAACCAGTACACCAATAGCATT
GGGAACTTTGAAAGAGAATTTAAACGCCGAAAAAAAGACATACTAGGAGAGTTAAGTTAGTTTTTGATAAAGTAGGGTTG
TCTGCTAGACCAAAAAGTCCTTTAGATCCTAAGAAGGATGGAGAATCCCTTTCATACTCTATGCTGCCTTTGAGTGATGG
TCCAGAAGGCTCCCATAATCATCCTCAGATGATAAGAGGTCGTCTGTGTGATGACAGCAAACCTGAGACCTTCAACCAGC
TGTGGACTGTTGAAGAACAGAAAAAACTCGAACAGCTACTCCTGAAATACCCTCCTGAAGAAGTAGAATCTTGGCGGTGG
CAGAAGATTGCTGATGAACTGGGCAACCAGACAGCCAAACAGGTTGCCAGTCGTGTACAGAAGTATTTCATAAAGCTAAC
AAAAGCCGGCATACCAGTTCCAGGCAGAACACCTAACTTATATATATACTCCAGAAAGTCCTCAACAAGCAGGCGACAGC
ACCCCCTTAATAAGCACCTCTTTAAACCTTCCACTTTCATGACTTCACATGAGCCACCAGTGTACATGGATGAAGATGAT
GACCGGTCTTGTCTCCATAGCCACATGAGCACTGCTGCTGAGGAGGCCTCAGATGATAAAAGCATTCCTATCATATATAG
GAGTTTACCTGAATATAAAGAACTATTACAGTTTAAAAAGTTAAAAAAGCAGAAACTTCAACAAATGCAAGCGGAAAGTG
GGTTTGTGCAGCATGTAGGCTTTAAGTCTGATAACTGTGGTGTGGAACCTAACCAAGGAGTCCGGTGGCACTGCCAGGAC
TGTCCTCCAGAAATGTCTTTGGATTTCTGTGACTCTTGTTCAGACTGCCCACATGAAACAGATACTCACAAGGAAGACCA
CCAGTTAGAACCTGTTTATAAGTCAGAGACGTTCTTAGACAGAGATTACTGTGTGTCCCAGGGCACCAGGTATAGTTACA
TGGACCCCAACTACTTCCCAGGCAACAGA
ORF - retro_mmus_3708 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.19 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MIDLWLYSYQRLLQTIAVLEAQRSQAVQDLESLGKHQREALKNPIGFVEKLQKKADIGLPYPQRVVQLPE |
| MIDLWLYSYQRLLQTIA.LEAQ.SQAVQDLESLGKH.REALKNPIGFVEKLQKKADIGLPYPQRVVQLPE | |
| Retrocopy | MIDLWLYSYQRLLQTIAALEAQCSQAVQDLESLGKHEREALKNPIGFVEKLQKKADIGLPYPQRVVQLPE |
| Parental | IMWDQYTN-SLGNFEREFKH-RKRHTRRVKLVFDKVGLPARPKSPLDPKKDGESLSYSMLPLSDGPEGSH |
| IMW.QYTN..LG..........KRHTRRVKLVFDKVGL.ARPKSPLDPKKDGESLSYSMLPLSDGPEGSH | |
| Retrocopy | IMWNQYTN>ALGTLKENLNA>KKRHTRRVKLVFDKVGLSARPKSPLDPKKDGESLSYSMLPLSDGPEGSH |
| Parental | NRPQMIRGRLCDDSKPETFNQLWTVEEQKKLEQLLLKYPPEEVESRRWQKIADELGNRTAKQVASRVQKY |
| N.PQMIRGRLCDDSKPETFNQLWTVEEQKKLEQLLLKYPPEEVES.RWQKIADELGN.TAKQVASRVQKY | |
| Retrocopy | NHPQMIRGRLCDDSKPETFNQLWTVEEQKKLEQLLLKYPPEEVESWRWQKIADELGNQTAKQVASRVQKY |
| Parental | FIKLTKAGIPVPGRTPNLYIYSRKSSTSRRQHPLNKHLFKPSTFMTSHEPPVYMDEDDDRSCLHSHMSTA |
| FIKLTKAGIPVPGRTPNLYIYSRKSSTSRRQHPLNKHLFKPSTFMTSHEPPVYMDEDDDRSCLHSHMSTA | |
| Retrocopy | FIKLTKAGIPVPGRTPNLYIYSRKSSTSRRQHPLNKHLFKPSTFMTSHEPPVYMDEDDDRSCLHSHMSTA |
| Parental | AEEASDEESIPIIYRSLPEYKELLQFKKLKKQKLQQMQAESGFVQHVGFKCDNCGVEPIQGVRWHCQDCP |
| AEEASD..SIPIIYRSLPEYKELLQFKKLKKQKLQQMQAESGFVQHVGFK.DNCGVEP.QGVRWHCQDCP | |
| Retrocopy | AEEASDDKSIPIIYRSLPEYKELLQFKKLKKQKLQQMQAESGFVQHVGFKSDNCGVEPNQGVRWHCQDCP |
| Parental | PEMSLDFCDSCSDCPHETDIHKEDHQLEPVYKSETFLDRDYCVSQGTSYSYLDPNYFPANR |
| PEMSLDFCDSCSDCPHETD.HKEDHQLEPVYKSETFLDRDYCVSQGT.YSY.DPNYFP.NR | |
| Retrocopy | PEMSLDFCDSCSDCPHETDTHKEDHQLEPVYKSETFLDRDYCVSQGTRYSYMDPNYFPGNR |
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 | 60 .91 RPM |
| SRP007412_cerebellum | 0 .26 RPM | 48 .46 RPM |
| SRP007412_heart | 0 .06 RPM | 34 .93 RPM |
| SRP007412_kidney | 0 .33 RPM | 57 .09 RPM |
| SRP007412_liver | 0 .05 RPM | 29 .93 RPM |
| SRP007412_testis | 0 .27 RPM | 40 .25 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3708 was not detected
No EST(s) were mapped for retro_mmus_3708 retrocopy.
No TSS is located nearby retro_mmus_3708 retrocopy 5' end.
retro_mmus_3708 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3708 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000039068 | 1 retrocopy |
retro_mmus_3708 ,
|
| Oryctolagus cuniculus | ENSOCUG00000002167 | 1 retrocopy |