RetrogeneDB ID: | retro_mdom_864 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 2:244558523..244560476(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMODG00000000274 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CCNT2 | ||
| Ensembl ID: | ENSMODG00000000727 | ||
| Aliases: | None | ||
| Description: | cyclin T2 [Source:HGNC Symbol;Acc:1600] |
Retrocopy-Parental alignment summary:
>retro_mdom_864
ATGGCGTCGGGCCGTGGGGCTTCTTCTCGCTGGTTCTTCAGCCGGGAGCAGCTGGAGAACACGCCGAGCCGCCGCTGCGG
GGTGGAGGCGGATAAAGAGCTCTCGTACCGCCAGCAGGCGGCCAACTTTATCCAAGATATGGGGCAGCGTCTCAATGTCT
CTCAACTTACAATAAATACTGCAATTGTTTACATGCACAGGTTTTATATGCACCATTCTTTCACAAAGTTTAACAGAAAT
ATAATAGCACCTACTGCATTATTCTTGGCTGCAAAAGTAGAAGAACAGCCAAGAAAACTTGAACATGTCATCAAAGTAGC
ACATGCCTGTCTTCATCAAGAGCTACTGTTGGACACAAAGAGTGAAGCATACCTTCAGCAGACCCAAGAACTGGTTATAC
TTGAAACTATAATGCTACAAACTCTGGGTTTTGAGATCACCATTGAACACCCACATACAGATGTGGTGAAATGTACCCAG
TTAGTGAGAGCAAGCAAGGATTTGGCACAGACATCCTATTTCATGGCTACCAACAGTCTACATCTTACTACCTTCTGCCT
TCAATATAAACCAACAGTGATAGCATGTGTGTGCATTCATTTGGCTTGCAAGTGGTCCAATTGGGAGATTCCTGTATCTA
CTGATGGAAAGCATTGGTGGGAATATGTGGATCCATCAGTTACCTTAGAATTACTAGATGAATTAACTCACGAGTTCCTA
CAAATTTTGGAGAAAACTCCTAATAGATTGAAGAGGATACGAAACTGGAGGGCTACTCAGGCGGCTAGAAAACCTAAAGG
GGATGGACAGGTGTCTGAAACAGCTCTTCTTGGTTCATCTCTGGTACAGAATTCCATTTTAGTAGATAGTGTTACTGGTG
TGACTACAAATGCAAGCTTTCAAAAACCATCTACATCAGCATTTCCTGCACCAGTACCTCTGAATTCAGGAAATATTTCT
GTTCAAGATACTCATGCATCTGATAATTTGACAATACTAACCACAGGAATGCCAAGTACCTCATACAGTTTGGCATCACA
CCAAGAATGGCCTCAGCATCAAGAACCAACAAGGACAGAACAAATATATTCACAGAAACAGGAGGCTCCGATGTCTGGTA
GTCAATACAACATCAACTTCCAGCAAGGACCTGCTGGGCCATTACATTCAGGATTACATCACAGGTCTGACAAACTGTCT
GATCATTCTTCAGTTAAACAAGAATATACTCACAAGGCAGGAAGCAGCAAACACCATGGGCCAGTTTCTGCTGCTCCTGT
AATAGTTCCTCAGAAAATGTCGTTAGATAAATATAGAGAGAAACGAAAGCTAGAAACACTTGAACTGGATGTAAGGGAAC
ACTATGTAGCTGCCCAAACAGAGCAGCCCCACAAAAAGCACATGCAATTGCAGGCAGCCAGCAGCAGTTCTGTAACTTCT
CCCATTAAAATGAAAATTCCTATTGCGAATGCAGAGAAACCGGAAAAATACATGTTGGATAAAAAAGAAAAGAGTGGATC
ACTTAAACTGCGTATTCCAATTCCCCCCACTGATAAAATTTCTAGTAAAGAAGAACTGAAAATGAAAATAAAAGTTTCTT
CCTCGGAAAGACACAGCTCTTCTGATGAGGGCAGTGGAAAGAGCAAGCATTCAAGCCCACATGTGAGTAAAGACCACAAA
GAAAAGCACAAGGAACATTCCTCCAACCGCCATCACAGTAGCAGCCACAAGCATTCCCATTCACATAGTGGCAGCAGTAG
TAGTGGCAGTAAGCATAGTACTGACGGAATACCACCCACGGTTCTGAGGAGTCCTGTTGGCCTGAGTAGTGATGGTGGTA
ATTCCTCTAGTTCCAGTGCTGCAAGAAAGAAGTTGCACATCAATGATGCGTCTCACAACCACCACTCCAAAATGAGCAAA
AGTTCCAAAAGTTCAGGTGGGCTACGGACATCT
ORF - retro_mdom_864 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.23 % |
| Parental protein coverage: | 88.69 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MASGRGASSRWFFSREQLENTPSRRCGVEADKELSYRQQAANFIQDMGQRLNVSQLTINTAIVYMHRFYM |
| MASGRGASSRWFFSREQLENTPSRRCGVEADKELSYRQQAANFIQDMGQRLNVSQLTINTAIVYMHRFYM | |
| Retrocopy | MASGRGASSRWFFSREQLENTPSRRCGVEADKELSYRQQAANFIQDMGQRLNVSQLTINTAIVYMHRFYM |
| Parental | HHSFTKFNRNIIAPTALFLAAKVEEQPRKLEHVIKVAHACLHQELLLDTKSEAYLQQTQELVILETIMLQ |
| HHSFTKFNRNIIAPTALFLAAKVEEQPRKLEHVIKVAHACLHQELLLDTKSEAYLQQTQELVILETIMLQ | |
| Retrocopy | HHSFTKFNRNIIAPTALFLAAKVEEQPRKLEHVIKVAHACLHQELLLDTKSEAYLQQTQELVILETIMLQ |
| Parental | TLGFEITIEHPHTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEI |
| TLGFEITIEHPHTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEI | |
| Retrocopy | TLGFEITIEHPHTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEI |
| Parental | PVSTDGKHWWEYVDPSVTLELLDELTHEFLQILEKTPNRLKRIRNWRATQAARKPKGDGQVSETALLGSS |
| PVSTDGKHWWEYVDPSVTLELLDELTHEFLQILEKTPNRLKRIRNWRATQAARKPKGDGQVSETALLGSS | |
| Retrocopy | PVSTDGKHWWEYVDPSVTLELLDELTHEFLQILEKTPNRLKRIRNWRATQAARKPKGDGQVSETALLGSS |
| Parental | LVQNSILVDSVTGVTTNASFQKPSTSAFPAPVPLNSGNISVQDTHASDNLTILTTGMPSTSYSLASHQEW |
| LVQNSILVDSVTGVTTNASFQKPSTSAFPAPVPLNSGNISVQDTHASDNLTILTTGMPSTSYSLASHQEW | |
| Retrocopy | LVQNSILVDSVTGVTTNASFQKPSTSAFPAPVPLNSGNISVQDTHASDNLTILTTGMPSTSYSLASHQEW |
| Parental | PQHQEPTRTEQIYSQKQEAPMSGSQYNINFQQGPAGPLHSGLHHRSDKLSDHSSVKQEYTHKAGSSKHHG |
| PQHQEPTRTEQIYSQKQEAPMSGSQYNINFQQGPAGPLHSGLHHRSDKLSDHSSVKQEYTHKAGSSKHHG | |
| Retrocopy | PQHQEPTRTEQIYSQKQEAPMSGSQYNINFQQGPAGPLHSGLHHRSDKLSDHSSVKQEYTHKAGSSKHHG |
| Parental | PVSAAPVIVPQKMSLDKYREKRKLETLELDVREHYVAAQTEQPHKKHMQLQAASSSSVTSPIKMKIPIAN |
| PVSAAPVIVPQKMSLDKYREKRKLETLELDVREHYVAAQTEQPHKKHMQLQAASSSSVTSPIKMKIPIAN | |
| Retrocopy | PVSAAPVIVPQKMSLDKYREKRKLETLELDVREHYVAAQTEQPHKKHMQLQAASSSSVTSPIKMKIPIAN |
| Parental | AEKPEKYMLDKKEKSGSLKLRIPIPPTDKSSSKEELKMKIKVSSSERHSSSDEGSGKSKHSSPHVSKDHK |
| AEKPEKYMLDKKEKSGSLKLRIPIPPTDK.SSKEELKMKIKVSSSERHSSSDEGSGKSKHSSPHVSKDHK | |
| Retrocopy | AEKPEKYMLDKKEKSGSLKLRIPIPPTDKISSKEELKMKIKVSSSERHSSSDEGSGKSKHSSPHVSKDHK |
| Parental | EKHKEHSSNRHHSSSHKHSHSHSGSSSSGSKHSTDGIPPTVLRSPVGLSSDGGNSSSSSAARKKLHINDA |
| EKHKEHSSNRHHSSSHKHSHSHSGSSSSGSKHSTDGIPPTVLRSPVGLSSDGGNSSSSSAARKKLHINDA | |
| Retrocopy | EKHKEHSSNRHHSSSHKHSHSHSGSSSSGSKHSTDGIPPTVLRSPVGLSSDGGNSSSSSAARKKLHINDA |
| Parental | SHNHHSKMSKSSKSSGSSSSS |
| SHNHHSKMSKSSKSSG....S | |
| Retrocopy | SHNHHSKMSKSSKSSGGLRTS |
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 .00 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .00 RPM |
| SRP007412_testis | 0 .00 RPM | 0 .00 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_864 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_864 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 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000000727 | 2 retrocopies |
retro_mdom_1109, retro_mdom_864 ,
|