RetrogeneDB ID: | retro_mdom_1721 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 7:75675210..75677229(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMODG00000003138 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SEC63 | ||
| Ensembl ID: | ENSMODG00000018012 | ||
| Aliases: | None | ||
| Description: | SEC63 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:21082] |
Retrocopy-Parental alignment summary:
>retro_mdom_1721
GTTTTTATTCCTTGCATACAAAGTTTCCAAAACAGAGAATATCAAGAATACAACCCTTATGAAGTCTTAAATTTGGATCC
TGGGGCAACAGTAACAGAGATTAAGAAACAATATCGTTTACTGTCACTTAAATACCATCCAGATAAAGGAGGAGATGAAG
TGATGTTCATGAGAATAGCAAAGGCCTATGCTGCTTTAACTGATGAAGAGTCTCGGAAAAATTGGGAAGAATATGGAAAT
CCAGATGGGCCACAAGCCACAAGTTCTGGAATTGCTTTGCCAGCTTGGATTGTGGATCAGAAGAACTCAATTTTGGTTTT
GCTTGTATATGGGTTGGCATTTATGGTTATCCTTCCAGTTGTAGTGGGCTCTTGGTGGTATAGATCAATACGCTATAGTG
GAGACCAGATCTTAATTCGCACAACTCAAATCTATACATACTTTGTGTATAAAACCCGAAACATGGATATGAAACGTCTC
ATAATGGTTTTAGCTGGGGCCTCTGAATTTGATCCTCAGTATAATAAAGATGCCACAAGCAGACCAGCTGATAATATTCA
GATACCACAGCTAATCAGAGAAATTGGCAGTATTAATTTAAAGAAGAATGAGCCTCCACTTACTTGCCCGTACAGCTTGA
AGGCCAGAGTTCTTTTACTATCTCATCTTGCTAGGATGAAAATTCCTGAAACACTTGAAGAAGATCAACAATTTGTCCTG
AAAAAATGCCCTGCCTTACTTCAAGAAATGGTTAATGTAATCTGTCAACTAATAATAATGGCTCGGAGCCGTGAAGAAAG
GGAGTTTCGTGCTCCAACTTTGGGATCCCTGGAAAACTGTATGAAGCTTTCCCAGATGTCTGTTCAAGGGCTTCAGCAAT
TTAAATCTCCCCTTCTTCAGCTCCCTCATATTGAAGAGGACAATCTTAGAAGGGTTTCTAATCATAAAAAGTTTAAAATC
AAAACTATCCAGGATTTAGTGAGTTTAAAAGAATCTGATCGCCGCAACTTACTACACTTCCTAGAAGATGAAAAATATGA
AGAAGTTATGGCTGTCCTTGGGAGTTTTCCATTTGTGACAATGGACATAAAATCACAGGTATTAGATGATGAAGATAGCA
ATAATATCACAGTAGGATCTCTTGTCACAGTATTGGTCAAATTGACAAAGCAGACAATGGCAGAAGTATTTGAAAAGGAA
CAGTCCATCTGTGCTGCAGAAGAGCAGCCAGCAGAAGATGGGCAAGGTGATGCAAACAAAAATAAGAGTAAAGGATGGCA
GCAGAAGAGTAAAGGACCTAAGAAAACTGCTAAATCAAAAAAAAAGAAACCTTTGAAAAAAAAGACAGCATCTGTTCCAT
TGCCTCAGACAAAGCAGCAGAAGCAAAAGCAGGCAAATGGGATTGTTGGGAGTGAAGCTGCCATAAAAGAAAATGAAGAT
GACATATCTGACAAAGGCAGTGACTCTGAGGAAGAAGAAACAAATAAGGACTCCCAAAGTGAAAAAGATGATGGAAGTGA
CCGAGACTCTGACAGAGAACAAGATGAAAAACAAAACAAAGATGATGAAGCAGAGTGGCAAGAATTGCAACAAAGTATAC
AGCGGAAGGAAAGAGCTCTGCTAGAAACCAAATCAAAGATAACACACCCGGTTTACAGTCTTTACTTTCCTGAGGAAAAA
CAGGAGTGGTGGTGGCTTTATATTGCTGATAGAAAGGAACAAACATTGATCTCTATGCCATATCACGTGTGCACATTAAA
AGATATGGAAGAGGTAGAACTGAAATTCCCTGCTCCAGGAAAACCTGGAAATTATCAGTATACAGTGTATCTAAGATCAG
ATTCCTATATGGGTTTGGACCAGATTAAACCATTGAAGTTGGAAGTTCATGAAGCTAAGCCAGTGCCAGAAAATCATCCA
CAATGGGATACAGCAATAGAGGGAGATGTAGACCAGGAAGATAGTGAAGGCTTTGAAGATAGTTTTGAAGAAGAAGAGGA
GGAAGAAGATGATGATGAC
ORF - retro_mdom_1721 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.29 % |
| Parental protein coverage: | 88.67 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LFLAYKVSKTDREYQEYNPYEVLNLDPGATVTEIKKQYRLLSLKYHPDKGGDEVMFMRIAKAYAALTDEE |
| .F.....S...REYQEYNPYEVLNLDPGATVTEIKKQYRLLSLKYHPDKGGDEVMFMRIAKAYAALTDEE | |
| Retrocopy | VFIPCIQSFQNREYQEYNPYEVLNLDPGATVTEIKKQYRLLSLKYHPDKGGDEVMFMRIAKAYAALTDEE |
| Parental | SRKNWEEYGNPDGPQATSFGIALPAWIVDQKNSILVLLVYGLAFMVILPVVVGSWWYRSIRYSGDQILIR |
| SRKNWEEYGNPDGPQATS.GIALPAWIVDQKNSILVLLVYGLAFMVILPVVVGSWWYRSIRYSGDQILIR | |
| Retrocopy | SRKNWEEYGNPDGPQATSSGIALPAWIVDQKNSILVLLVYGLAFMVILPVVVGSWWYRSIRYSGDQILIR |
| Parental | TTQIYTYFVYKTRNMDMKRLIMVLAGASEFDPQYNKDATSRPADNIQIPQLIREIGSINLKKNEPPLTCP |
| TTQIYTYFVYKTRNMDMKRLIMVLAGASEFDPQYNKDATSRPADNIQIPQLIREIGSINLKKNEPPLTCP | |
| Retrocopy | TTQIYTYFVYKTRNMDMKRLIMVLAGASEFDPQYNKDATSRPADNIQIPQLIREIGSINLKKNEPPLTCP |
| Parental | YSLKARVLLLSHLARMKIPETLEEDQQFVLKKCPALLQEMVNVICQLIIMARSREEREFRAPTLGSLENC |
| YSLKARVLLLSHLARMKIPETLEEDQQFVLKKCPALLQEMVNVICQLIIMARSREEREFRAPTLGSLENC | |
| Retrocopy | YSLKARVLLLSHLARMKIPETLEEDQQFVLKKCPALLQEMVNVICQLIIMARSREEREFRAPTLGSLENC |
| Parental | MKLSQMSVQGLQQFKSPLLQLPHIEEDNLRRVSNHKKFKIKTIQDLVSLKESDRRNLLHFLEDEKYEEVM |
| MKLSQMSVQGLQQFKSPLLQLPHIEEDNLRRVSNHKKFKIKTIQDLVSLKESDRRNLLHFLEDEKYEEVM | |
| Retrocopy | MKLSQMSVQGLQQFKSPLLQLPHIEEDNLRRVSNHKKFKIKTIQDLVSLKESDRRNLLHFLEDEKYEEVM |
| Parental | AVLGSFPFVTMDIKSQVLDDEDSNNITVGSLVTVLVKLTRQTMAEVFEKEQSICAAEEQPAEDGASDANK |
| AVLGSFPFVTMDIKSQVLDDEDSNNITVGSLVTVLVKLT.QTMAEVFEKEQSICAAEEQPAEDG..DANK | |
| Retrocopy | AVLGSFPFVTMDIKSQVLDDEDSNNITVGSLVTVLVKLTKQTMAEVFEKEQSICAAEEQPAEDGQGDANK |
| Parental | NKSKGWQQKSKGPKKTAKSKKKKPLKKKTASVPLPQTKQQKQKQANGIVGSEAAIKEDEDDISDKGSDSE |
| NKSKGWQQKSKGPKKTAK..........TASVPLPQTKQQKQKQANGIVGSEAAIKE.EDDISDKGSDSE | |
| Retrocopy | NKSKGWQQKSKGPKKTAKXXXXXXXXXXTASVPLPQTKQQKQKQANGIVGSEAAIKENEDDISDKGSDSE |
| Parental | EEETNKDSQSEKDDGSDRDSDREQDEKQNKDDEAEWQELQQSIQRKERALLETKSKITHPVYSLYFPEEK |
| EEETNKDSQSEKDDGSDRDSDREQDEKQNKDDEAEWQELQQSIQRKERALLETKSKITHPVYSLYFPEEK | |
| Retrocopy | EEETNKDSQSEKDDGSDRDSDREQDEKQNKDDEAEWQELQQSIQRKERALLETKSKITHPVYSLYFPEEK |
| Parental | QEWWWLYIADRKEQTLISMPYHVCTLKDMEEVELKFPAPGKPGNYQYTVYLRSDSYMGLDQIKPLKLEVH |
| QEWWWLYIADRKEQTLISMPYHVCTLKDMEEVELKFPAPGKPGNYQYTVYLRSDSYMGLDQIKPLKLEVH | |
| Retrocopy | QEWWWLYIADRKEQTLISMPYHVCTLKDMEEVELKFPAPGKPGNYQYTVYLRSDSYMGLDQIKPLKLEVH |
| Parental | EAKPVPENHPQWDTAIEGDEDQEDSEGFEDSFEEEEEEEDDDD |
| EAKPVPENHPQWDTAIEGD.DQEDSEGFEDSFEEEEEEEDDDD | |
| Retrocopy | EAKPVPENHPQWDTAIEGDVDQEDSEGFEDSFEEEEEEEDDDD |
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_1721 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1721 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 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000018012 | 1 retrocopy |
retro_mdom_1721 ,
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