RetrogeneDB ID: | retro_mdom_1957 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | Un:24410923..24412969(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMODG00000021341 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MTMR10 | ||
| Ensembl ID: | ENSMODG00000011784 | ||
| Aliases: | None | ||
| Description: | myotubularin related protein 10 [Source:HGNC Symbol;Acc:25999] |
Retrocopy-Parental alignment summary:
>retro_mdom_1957
TTTCAGAAATTTCATTATACAAACCTTCTCCTTGGTGAACATGATGTACCTTTAACATGTATTGAGCAAATTGTAACAGT
AAATGACAACAAAAGGAAACAGAAGATACTAGGCCCCAACCAGAAACTCAAATTTAATCCTACAGAGCTAATTATCTATT
GTAAAGATTTCAGAATTGTCAGATTTCGCTTTGATGAAGCAGGTCCTGAAAGTGCCAAAAAGGTGTGCCTTGCGATAGCT
CATTATTCTCAGCCAACTGATCTCCAGCTACTCTTTGCATTTGAATACGTTGGGGAAAAGTACCACAATACAGCTAAAAA
TATTAATGGAATAGACTCTGGAAGTGGAGGAATACCTGGTGGTAATAGTCAAAAAACTCCTTTATTTGAAACTTTCTCTG
ATTGGGATAGAGAAATCAAAAGGACAGGTGCCTCAGAATGGAGAGTTTGTTCAATTAATGAGGGCTACATGATTTCTACT
TGCCTTCCAGAATATTTTGTAGTTCCATCTTCTTTGGCAGATCAAGATCTAAAACTCTATTCTCATTCTGTTTTTGGGAG
GCGGATGCCATTATGGTGCTGGAATCACTCTAATGGCAGTGCTCTTATAAGAATGGCCCTCATAAAAGATGTATTGCAAC
AGAAAAAAATAGATCAAAGGATTTGTACTGCAATAACCAAAAGTCATCCACAGAGGAGTGATGTGTACAAATCTGATTTG
GATAAGAATTTGCCTAGTATTCAAGAAATACAAGCTGCATTTGTAAAACTTAAGCAACTCTGTGTTGATGAGCCTTATGA
GGAAACAGAAGTGAAATGGTTGTCTTCACTGGAAAATACTCGCTGGTTAGAGTATGTTAGAGCATTCCTAAAGTATTCTG
CTGAGCTTGTATATGTGCTGGAAAGTAAACATCTTTCAGTTATCCTTAGAGAGGAAGAAGGAAGGGATCTGAGTTGTTTC
GTAGCTTCTCTCATTCAAGTGATGCTGGATCCTCATTTTCGAACAATTACTGGATTTCAAAGTTTGATACAGAAAGAATG
GGTCATGGCAGGATATCGATTTCTAGACAGATGTAACCACTTAAATAGATCTGCAAAAGAGTCTCCCTTATTCTTGTTAT
TTCTGGACTCCATCTGGCAGCTGTTAGAGCAATATCCAGCAGCCTTTGAATTTTCAGAAACTTATTTAATGTTGCTGTAT
GACAGTACACGGATCTCATTGTTTGGCACTTTTCTTTTCAACTCTCCTCATCAGCGAGTAAAACAAAGCACAGAATTTGC
TATTAGCAAAAATATACAACTCGGTGATGAAAAGGGCTTAAAATTTCCGTCGGTTTGGGACTGGTCTCTTCAATTTGCAG
CAAAGGATCGCACCCTTTTTAATAATCCCTTATACATTGGAAAGAGTGCACCATGTGTACAAAATGGGTCAGTGAAATCA
TTTAAGCGGACAAAGAAAAATTATAGCTCTACATTAAGAGGAATGCCACCTTCCTTTAAGAATGGACTCATCAATGATCA
AGATTTGCTTCCAAGGAGAAATTCACTAATATTGAAATTAAAGACTGATATAGAGCAAACTGACAGCCAGAGCACTGATA
TGGAGCAATATTTTAGAGACTGGTTTTCAAAACCTGTTGACCTGCATGGTGTAATTCTACCCCGCATTTCGGGAATACAC
ATAAAACTGTGGAAACTCTGCTACTTCCGTTGGGTTCCAGAGGCTCAGATTAATAATGGTGGCTTCATTATAGCATTTCA
TAGAATATCTCTTCTGACAGATGAAATAGATATGCTCAGCAGGAGTCTTCGACAGTACAAGAGCAATTCCTCGCAATCCA
GCTATTCAGAACTGGATCAGAGTAGGATGTACTTTAAAGCAAATGGTATAAATGATACATCTGGGACGCCAGAGTTTCTT
TCCTCTTCATTTCCGTTTTCACCTATAGGGAACCTTTGCAGAAGAAGCATTTTAGGAACACCATTAAGCAAATTTTTAAA
TGGTGCCAAAATATGGCTGTCTACTGAGACACTAGCAAATGAGGAC
ORF - retro_mdom_1957 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.71 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | FQKFHYTNLLLGEHDVPLTCIEQIVTVNDNKRKQKILGPNQKLKFNPTELIIYCKDFRIVRFRFDEAGPE |
| FQKFHYTNLLLGEHDVPLTCIEQIVTVNDNKRKQKILGPNQKLKFNPTELIIYCKDFRIVRFRFDEAGPE | |
| Retrocopy | FQKFHYTNLLLGEHDVPLTCIEQIVTVNDNKRKQKILGPNQKLKFNPTELIIYCKDFRIVRFRFDEAGPE |
| Parental | SAKKVCLAIAHYSQPTDLQLLFAFEYVGEKYHNTAKNINGIDSGSGGIPGGNSQKTPLFETFSDWDREIK |
| SAKKVCLAIAHYSQPTDLQLLFAFEYVGEKYHNTAKNINGIDSGSGGIPGGNSQKTPLFETFSDWDREIK | |
| Retrocopy | SAKKVCLAIAHYSQPTDLQLLFAFEYVGEKYHNTAKNINGIDSGSGGIPGGNSQKTPLFETFSDWDREIK |
| Parental | RTGASEWRVCSINEGYMISTCLPEYFVVPSSLADQDLKLYSHSFFGRRMPLWCWNHSNGSALIRMALIKD |
| RTGASEWRVCSINEGYMISTCLPEYFVVPSSLADQDLKLYSHS.FGRRMPLWCWNHSNGSALIRMALIKD | |
| Retrocopy | RTGASEWRVCSINEGYMISTCLPEYFVVPSSLADQDLKLYSHSVFGRRMPLWCWNHSNGSALIRMALIKD |
| Parental | VLQQKKIDQRICTAITKSHPQRSDVYKSDLDKNLPSIQEIQAAFVKLKQLCVDEPYEETEVKWLSSLENT |
| VLQQKKIDQRICTAITKSHPQRSDVYKSDLDKNLPSIQEIQAAFVKLKQLCVDEPYEETEVKWLSSLENT | |
| Retrocopy | VLQQKKIDQRICTAITKSHPQRSDVYKSDLDKNLPSIQEIQAAFVKLKQLCVDEPYEETEVKWLSSLENT |
| Parental | RWLEYVRAFLKYSAELVYVLESKHLSVILREEEGRDLSCFVASLIQVMLDPHFRTITGFQSLIQKEWVMA |
| RWLEYVRAFLKYSAELVYVLESKHLSVILREEEGRDLSCFVASLIQVMLDPHFRTITGFQSLIQKEWVMA | |
| Retrocopy | RWLEYVRAFLKYSAELVYVLESKHLSVILREEEGRDLSCFVASLIQVMLDPHFRTITGFQSLIQKEWVMA |
| Parental | GYRFLDRCNHLNRSAKESPLFLLFLDSIWQLLEQYPAAFEFSETYLMLLYDSTRISLFGTFLFNSPHQRV |
| GYRFLDRCNHLNRSAKESPLFLLFLDSIWQLLEQYPAAFEFSETYLMLLYDSTRISLFGTFLFNSPHQRV | |
| Retrocopy | GYRFLDRCNHLNRSAKESPLFLLFLDSIWQLLEQYPAAFEFSETYLMLLYDSTRISLFGTFLFNSPHQRV |
| Parental | KQSTEFAISKNIQLGDEKGLKFPSVWDWSLQFAAKDRTLFNNPLYIGKSAPCVQNGSVKSFKRTKKNYSS |
| KQSTEFAISKNIQLGDEKGLKFPSVWDWSLQFAAKDRTLFNNPLYIGKSAPCVQNGSVKSFKRTKKNYSS | |
| Retrocopy | KQSTEFAISKNIQLGDEKGLKFPSVWDWSLQFAAKDRTLFNNPLYIGKSAPCVQNGSVKSFKRTKKNYSS |
| Parental | TLRGMPPSFKNGLINDQDLLPRRNSLILKLKTDIEQTDSQSTDMEQYFRDWFSKPVDLHGVILPRISGIH |
| TLRGMPPSFKNGLINDQDLLPRRNSLILKLKTDIEQTDSQSTDMEQYFRDWFSKPVDLHGVILPRISGIH | |
| Retrocopy | TLRGMPPSFKNGLINDQDLLPRRNSLILKLKTDIEQTDSQSTDMEQYFRDWFSKPVDLHGVILPRISGIH |
| Parental | IKLWKLCYFRWVPEAQINNGGFITAFHRISLLTDEIDMLSRSLRQYKSNSSQSSYSELDQSRMYFKANGI |
| IKLWKLCYFRWVPEAQINNGGFI.AFHRISLLTDEIDMLSRSLRQYKSNSSQSSYSELDQSRMYFKANGI | |
| Retrocopy | IKLWKLCYFRWVPEAQINNGGFIIAFHRISLLTDEIDMLSRSLRQYKSNSSQSSYSELDQSRMYFKANGI |
| Parental | NDTSGTPEFLSSSFPFSPIGNLCRRSILGTPLSKFLNGAKIWLSTETLANED |
| NDTSGTPEFLSSSFPFSPIGNLCRRSILGTPLSKFLNGAKIWLSTETLANED | |
| Retrocopy | NDTSGTPEFLSSSFPFSPIGNLCRRSILGTPLSKFLNGAKIWLSTETLANED |
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 | 8 .22 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 6 .86 RPM |
| SRP007412_heart | 0 .00 RPM | 5 .38 RPM |
| SRP007412_kidney | 0 .00 RPM | 27 .65 RPM |
| SRP007412_liver | 0 .00 RPM | 17 .12 RPM |
| SRP007412_testis | 0 .00 RPM | 7 .07 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_1957 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1957 was not experimentally validated.
Retrocopy orthology:
Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000012336 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000011784 | 2 retrocopies |
retro_mdom_1377, retro_mdom_1957 ,
|
| Ictidomys tridecemlineatus | ENSSTOG00000008851 | 1 retrocopy |