RetrogeneDB ID: | retro_cfam_1523 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 33:16957954..16959433(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCAFG00000010477 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MTMR12 | ||
| Ensembl ID: | ENSCAFG00000018909 | ||
| Aliases: | None | ||
| Description: | myotubularin related protein 12 [Source:HGNC Symbol;Acc:18191] |
Retrocopy-Parental alignment summary:
>retro_cfam_1523
GAAATTCATGCAAACGAGAAGGAAGTAACTCTTCACTTGTTGCCAGGTGAACAGCTGCTTTGTGAAGCCAGTACAGTGCT
GAAGTATGTCCAGGAGGATTCCTGTCAGCGTGGGATCTATGGGAAACTTGTGTGCACAGACTTCAAGATCGCCTTCTTGG
GCGATGATGAATCTGCGTTGGATAATGATGAGGCCCAATTTAAGAATAAGGTTATAGGAGAAAATGACATCACACTCCAC
TGCGTTGATCAGATTTATGGAGTGTTTGATGAGAAAAAGAAACCTCTTTTTGGACAATTGAAGAAATACCCTGAAAAACT
CATCATCCACTGCAAAGACCTTCGAGTGTTCCACTTTGGTCTGAGGTACACAAGAGAAGAGGAAGTCAAAAGGATTGTCA
GTGGCATAATTCATCATACCCAAGCTCCTAAACTGCTTAAAAGATTATTTCTGTTTTCCTATGCAGCTGCTGCACAAAAC
AATACAGCCACTGATCCCAAGAACCATACTGTAATGTTTGACACCCTTAAGGACTGGTGTTGGGAATTGGAGCGGACCAA
AGGCAACGTCAAGTACAAAGCAGTGAGTGTCAATGAAGGCTATAAAGTCTGTGTAAGATTGCCAGCATACTTTGTTGTCC
CTATTTCTCTTCCTGAAGAGGACGTGCTACGCTTTCAGGGTCACGGCATACCAATATGGTGCTGGTCCTGCCACAATGGA
TGTGCCCTTTTGAAAATGTCAGCACTGCCCAAAGAACAGGATGATGGCAGTTTACAAATCCAAAAGAGCTTCTTGGATGG
AATTTACAAGACCATCCACAGGCCACCCTATGAAATTGTTAAAACTGAAGACCTGTCAACCAACTTCCTGTCCTTGCAGG
ACATCCAGACTGCATACTCTAAATTTAAACAGCTGTTTCTGATAGATAATAGTACGGAATTTTGGGACACAGATATAAAA
TGGTTTTCTCTGTTGGAAAATAGCAGTTGGCTTGATATAATCAGACGTTGCCTGAAAAAAGCAATAGAGATTGCAGAATG
TCTAGAAGCACAAAACATGAACGTTCTTCTTTTAGAGGAGAATGCTTCAGACCTCTGCTGCCTCATTTCCTCTCTGGTAC
AAGTGATGATGGACCCCCACTGCAGAACCAGGGTTGGTTTCCAGAGCCTCGTCCAGAAGGAGTGGATCATGGGCGGCCAC
TGTTTCCTGGATCGCTGCAACCACCTCCGTCAAAGTGACAAAGAGGAGGTTCCCGTGTTCCTGCTGTTCTTAGATTGTGT
GTGGCAGCTGGTGCACCAGCATCCCCCAGCATTTGATTTCACGGAGACTTACTTGACTGTTTTGTCAGATAGTCTATACT
TACCTATTTTTAGCACCTTCTTCTTCAATTCGCCTCATCAAAAAGATATTAACATGGGTAGGGAACACCAGGATACACAG
AGCAAGCCTTTGAATCTGCTCACCGTGTGGGATTGGAAC
ORF - retro_cfam_1523 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.78 % |
| Parental protein coverage: | 68.47 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | EKEVTEKEVTLHLLPGEQLLCEASTVLKYVQEDSCQRGIYGKLVCTDFKIAFLGDDESALDNDEAQFKNK |
| E....EKEVTLHLLPGEQLLCEASTVLKYVQEDSCQRGIYGKLVCTDFKIAFLGDDESALDNDEAQFKNK | |
| Retrocopy | EIHANEKEVTLHLLPGEQLLCEASTVLKYVQEDSCQRGIYGKLVCTDFKIAFLGDDESALDNDEAQFKNK |
| Parental | VIGENDITLHCVDQIYGVFDEKKKPLFGQLKKYPEKLIIHCKDLRVFHFGLRYTKEEEVKRIVSGIIHHT |
| VIGENDITLHCVDQIYGVFDEKKKPLFGQLKKYPEKLIIHCKDLRVFHFGLRYT.EEEVKRIVSGIIHHT | |
| Retrocopy | VIGENDITLHCVDQIYGVFDEKKKPLFGQLKKYPEKLIIHCKDLRVFHFGLRYTREEEVKRIVSGIIHHT |
| Parental | QAPKLLKRLFLFSYAAAAQNNTATDPKNHTVMFDTLKDWCWELERTKGNVKYKAVSVNEGYKVCVRLPAY |
| QAPKLLKRLFLFSYAAAAQNNTATDPKNHTVMFDTLKDWCWELERTKGNVKYKAVSVNEGYKVCVRLPAY | |
| Retrocopy | QAPKLLKRLFLFSYAAAAQNNTATDPKNHTVMFDTLKDWCWELERTKGNVKYKAVSVNEGYKVCVRLPAY |
| Parental | FVVPISLPEEDVLRFQGHGIPIWCWSCHNGCALLKMSALPKEQDDGSLQIQKSFLDGIYKTIHRPPYEIV |
| FVVPISLPEEDVLRFQGHGIPIWCWSCHNGCALLKMSALPKEQDDGSLQIQKSFLDGIYKTIHRPPYEIV | |
| Retrocopy | FVVPISLPEEDVLRFQGHGIPIWCWSCHNGCALLKMSALPKEQDDGSLQIQKSFLDGIYKTIHRPPYEIV |
| Parental | KTEDLSTNFLSLQDIQTAYSKFKQLFLIDNSTEFWDTDIKWFSLLENSSWLDIIRRCLKKAIEIAECLEA |
| KTEDLSTNFLSLQDIQTAYSKFKQLFLIDNSTEFWDTDIKWFSLLENSSWLDIIRRCLKKAIEIAECLEA | |
| Retrocopy | KTEDLSTNFLSLQDIQTAYSKFKQLFLIDNSTEFWDTDIKWFSLLENSSWLDIIRRCLKKAIEIAECLEA |
| Parental | QNMNVLLLEENASDLCCLISSLVQVMMDPHCRTRVGFQSLVQKEWIMGGHCFLDRCNHLRQSDKEEVPVF |
| QNMNVLLLEENASDLCCLISSLVQVMMDPHCRTRVGFQSLVQKEWIMGGHCFLDRCNHLRQSDKEEVPVF | |
| Retrocopy | QNMNVLLLEENASDLCCLISSLVQVMMDPHCRTRVGFQSLVQKEWIMGGHCFLDRCNHLRQSDKEEVPVF |
| Parental | LLFLDCVWQLVHQHPPAFDFTETYLTVLSDSLYLPIFSTFFFNSPHQKDINMGREHQDTQSKPLNLLTVW |
| LLFLDCVWQLVHQHPPAFDFTETYLTVLSDSLYLPIFSTFFFNSPHQKDINMGREHQDTQSKPLNLLTVW | |
| Retrocopy | LLFLDCVWQLVHQHPPAFDFTETYLTVLSDSLYLPIFSTFFFNSPHQKDINMGREHQDTQSKPLNLLTVW |
| Parental | DWS |
| DW. | |
| Retrocopy | DWN |
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 |
|---|---|---|
| SRP012049_cerebellum | 0 .42 RPM | 8 .90 RPM |
| SRP017611_brain | 0 .79 RPM | 9 .61 RPM |
| SRP017611_kidney | 0 .73 RPM | 7 .92 RPM |
| SRP017611_liver | 0 .07 RPM | 0 .65 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1523 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1523 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1523 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 | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000018909 | 1 retrocopy |
retro_cfam_1523 ,
|
| Microcebus murinus | ENSMICG00000002269 | 1 retrocopy |