RetrogeneDB ID: | retro_mmus_2717 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 6:12857396..12858393(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000083620 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Hormad1 | ||
| Ensembl ID: | ENSMUSG00000028109 | ||
| Aliases: | Hormad1, 4921522K05Rik, Nohma | ||
| Description: | HORMA domain containing 1 [Source:MGI Symbol;Acc:MGI:1915231] |
Retrocopy-Parental alignment summary:
>retro_mmus_2717
GATCTCTGTGTCAAAATTCTGAAAGAAGATAAAAATTGTCCAGGTTCTTCACAGCTAGTGAAGTGGATGCTAGGATGCTA
GGATGCTTTACAGAAGAAATATCTAAGGATGATCATTCTAGCTGTATACACCAATCCAGGAGATCCTCAGACAATTTCAG
GATATTACCAGTTTAAATTCAAGTACACCAAAAATGGACCAATCATGGACTTTATAAGCAAAAATCAAAACAATAAATCT
AGTACAACATCTGCTGACAGCAAGAAAGCAAGCATTCCCCTCATTCGGAAGATTTATGTCTTAATGCAAAATCTAGGACC
ATTACCTAAAGCTGTTTGTCTGACCAGGAAACTTTTTTACTATGATGAAGTTACACCCCCAAATTACCAACCACCAGGTT
TTAAGGATGGTGACTGTGAAGGAGTAATATTTGATGGGAACCCTACATACTTAAATGTGGGAGAAGTCCCAACACCTTTT
CACACCCTCAGATTAAAAGTGACCACTGAGAAGGAACGAATGGAAAATATTGATTCAACCATACTAAAACCAAAAGAATC
AAGAACACAATTTGAAAAAATTCTAAGGGACAAAGATGATGTAGAAGATGAAAAATCATAATAATTTTGACATTAAAACT
AAAATGAACGAACAGAATGAAAACTCTGGAGCTTCTGAAATCAAAGAACCAAATTTAGATTGTAAGGAAGAAGAAACTAT
GCAATTCAAAAAGAGCCAAAGTCCTTCAATTTCTCATTGTCAGGTTGAACAGTTAGTCAGTAAAACATCTGAACTTGATG
TGTCTGAAAGCAAAACAAGAAGCGGAAAAATCTTTCAGAGTAAAATGGTAAATGGAAATAATCAACAAGGACAAACGTCT
AAAGAAAATTGGAAGAGAGGTCTTCGTCAATTTGGGAAAACAGTCCTTCACGTCTTGGAATCTAGTCAAGAGTCAGTGCT
GAAGAAAAGGAGAGTTAGTGAACCAAAGGAACATACC
ORF - retro_mmus_2717 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.79 % |
| Parental protein coverage: | 84.69 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | DLCVKILKEDKNCPGSSQLVKWMLGCYDALQKKYLRMIILAVYTNPGDPQTISECYQFKFKYTKNGPIMD |
| DLCVKILKEDKNCPGSSQLVK........LQKKYLRMIILAVYTNPGDPQTIS..YQFKFKYTKNGPIMD | |
| Retrocopy | DLCVKILKEDKNCPGSSQLVKXXXXXXXXLQKKYLRMIILAVYTNPGDPQTISGYYQFKFKYTKNGPIMD |
| Parental | FISKNQNNKSSTTSADTKKASILLIRKIYVLMQNLGPLPNDVCLTMKLFYYDEVTPPDYQPPGFKDGDCE |
| FISKNQNNKSSTTSAD.KKASI.LIRKIYVLMQNLGPLP..VCLT.KLFYYDEVTPP.YQPPGFKDGDCE | |
| Retrocopy | FISKNQNNKSSTTSADSKKASIPLIRKIYVLMQNLGPLPKAVCLTRKLFYYDEVTPPNYQPPGFKDGDCE |
| Parental | GVIFDGDPTYLNVGEVPTPFHTFRLKVTTEKERMENIDSTILKPKESKTQFEKILMDKDDVEDE-NHNNF |
| GVIFDG.PTYLNVGEVPTPFHT.RLKVTTEKERMENIDSTILKPKES.TQFEKIL.DKDDVEDE.NHNNF | |
| Retrocopy | GVIFDGNPTYLNVGEVPTPFHTLRLKVTTEKERMENIDSTILKPKESRTQFEKILRDKDDVEDE>NHNNF |
| Parental | DIKTKMNEQNENSGASEIKEPNLDCKEEETMQFKKSQSPSISHCQVEQLVSKTSELDVSESKTRSGKIFQ |
| DIKTKMNEQNENSGASEIKEPNLDCKEEETMQFKKSQSPSISHCQVEQLVSKTSELDVSESKTRSGKIFQ | |
| Retrocopy | DIKTKMNEQNENSGASEIKEPNLDCKEEETMQFKKSQSPSISHCQVEQLVSKTSELDVSESKTRSGKIFQ |
| Parental | SKMVNGNNQQGQTSKENRKRSLRQFRKTVLHVLESSQESVLKKRRVSEPKEHT |
| SKMVNGNNQQGQTSKEN.KR.LRQF.KTVLHVLESSQESVLKKRRVSEPKEHT | |
| Retrocopy | SKMVNGNNQQGQTSKENWKRGLRQFGKTVLHVLESSQESVLKKRRVSEPKEHT |
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 | 0 .00 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 0 .00 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .00 RPM |
| SRP007412_kidney | 0 .00 RPM | 0 .02 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .03 RPM |
| SRP007412_testis | 0 .32 RPM | 30 .65 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2717 was not detected
No EST(s) were mapped for retro_mmus_2717 retrocopy.
No TSS is located nearby retro_mmus_2717 retrocopy 5' end.
retro_mmus_2717 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2717 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 6 parental genes, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000000071 | 1 retrocopy | |
| Homo sapiens | ENSG00000143452 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000028109 | 2 retrocopies |
retro_mmus_1420, retro_mmus_2717 ,
|
| Otolemur garnettii | ENSOGAG00000005640 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000021160 | 1 retrocopy | |
| Tarsius syrichta | ENSTSYG00000006025 | 1 retrocopy |