RetrogeneDB ID: | retro_mdom_1242 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 4:65002507..65003173(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMODG00000002343 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ARRB1 | ||
| Ensembl ID: | ENSMODG00000007021 | ||
| Aliases: | None | ||
| Description: | arrestin, beta 1 [Source:HGNC Symbol;Acc:711] |
Retrocopy-Parental alignment summary:
>retro_mdom_1242
CCCGGGGAGCCGCCCATGGCCGAGACCACTTGTCAGTCTCCGATGTCTGACAAGCCCTTACACTTGGAAACCTCTCTGGA
CAAGGAGATCGACTACCTCGGGGAACCGATCAGTGTCAATGTCCATGTCACCAGCAACAACACCAAAACAGTGAAGAAGA
TAAAAATTCCAGTCCGTCAGTCTGCAGACATCTGCCTGTTCAACATGGCACATTACAAATGCCCCGTGGGTGTGGAGGAG
GCTGATGACATGGTGGCCCCAAGTTCAACATGCTGCAAAGTCTACACCCTCATCCCATTCTTGGCCAACAACTGTGAGAA
GCTAGACCTGGCCCTGGATGGCAAGCTGAAGCATGAAGACACCAACTTGGCTTCCAGTACCCTGTTGAGGGATGGCACAA
ATAAGGAGATCTTAGGAATCATCCTGTCCTACCAAGTCAAAGTGAAGCTGTTTGTTTCCCAAGGAGGCCTGTTGGGAGAT
CTCACATCCAATGATGTGAGGAGGGCTGTTGAACTTCCCTTCACCTTAATGCACCCGAAGCCCAGGGAAGAGCCTTTGTA
TGGAGAAGTTCCAGAGAGTGAAGCGCCCATAGATACCAATCTCATAGAGCTCGATACAAACGATGACGACATTGTCTTTG
AGGACATAGCTCGACAGAGACTGAAA
ORF - retro_mdom_1242 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.93 % |
| Parental protein coverage: | 52.38 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | PGPQPTAETTRQFLMSDKPLHLEASLDKEIYYHGEPISVNVHVTNNTNKTVKKIKISVRQYADICLFNTA |
| PG..P.AETT.Q..MSDKPLHLE.SLDKEI.Y.GEPISVNVHVT.N..KTVKKIKI.VRQ.ADICLFN.A | |
| Retrocopy | PGEPPMAETTCQSPMSDKPLHLETSLDKEIDYLGEPISVNVHVTSNNTKTVKKIKIPVRQSADICLFNMA |
| Parental | QYKCPVAVEEADDMVAPSSTFCKVYTLTPFLANNREKRGLALDGKLKHEDTNLASSTLLRDGTNKEILGI |
| .YKCPV.VEEADDMVAPSST.CKVYTL.PFLANN.EK..LALDGKLKHEDTNLASSTLLRDGTNKEILGI | |
| Retrocopy | HYKCPVGVEEADDMVAPSSTCCKVYTLIPFLANNCEKLDLALDGKLKHEDTNLASSTLLRDGTNKEILGI |
| Parental | IVSYKVKVKLVVSRGGLLGDLASSDV--AVELPFTLMHPKPREEPVRREGDHCMSLLEGTLKQLDHDDDD |
| I.SY.VKVKL.VS.GGLLGDL.S.DV..AVELPFTLMHPKPREEP...E...........L..LD..DDD | |
| Retrocopy | ILSYQVKVKLFVSQGGLLGDLTSNDVRRAVELPFTLMHPKPREEPLYGEVPESEAPIDTNLIELDTNDDD |
| Parental | IVFEDFARQRLK |
| IVFED.ARQRLK | |
| Retrocopy | IVFEDIARQRLK |
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_1242 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1242 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 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Felis catus | ENSFCAG00000011941 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000007021 | 1 retrocopy |
retro_mdom_1242 ,
|