RetrogeneDB ID: | retro_mdom_1099 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 3:106822164..106823403(-) | ||
| Located in intron of: | ENSMODG00000025607 | ||
Retrocopy information | Ensembl ID: | ENSMODG00000002471 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RBM41 | ||
| Ensembl ID: | ENSMODG00000002312 | ||
| Aliases: | None | ||
| Description: | RNA binding motif protein 41 [Source:HGNC Symbol;Acc:25617] |
Retrocopy-Parental alignment summary:
>retro_mdom_1099
ATGAAGAGGATAAACAGTAGCCTTTCCAGTGATGACCTTATTCTGGAGGACTTGGAGACAGAGGGAGAGAGGCAGCTAAG
AAGCCTTCTTCACCATCAGCTCGATACTTCTGTTTCTGTTGAGGAATGTGTATCTAAGAAGCAATGCTTTGCTCCTGCTG
CAGTGTACAAGCCCTTTGGTGAGGAGGCAGCTGGGGTTTTGAGCTTGTCCCAGTTTCAGGCACTACAGAAGAGTGACCAG
GAAATCGCATCTCTGAGGGACTTGGGTCTTACTGATAGAGAAATCATGCTGTGGAAAAATCGTGCTTCATTAGAGAGGGG
TACAGGGCTGGGAGCAACCCCTGAAGCAACACAGGACTGTCTTCGAGACATTGAAGAGAAGATCTCGGAGCATCAGCGCA
TCCTGGCTTTGCCACAGAGGTTTGCAGGGTGTAAACAGCTGAGCCGACGGGAGATGGAAATAGAAAAGGCTTTGTTTCAG
GGGAATGATCGCCATTCCTTCTTGAGGGCTCTCTATTACCAAGGTGAATCCCATAAGAGACTAGAGGCTGAGAAGGACCC
CATTAATAATCTGGAGACTGTTTACCAAGAGATGATGGCCAAACCCCATCTCAAAGAAGCTCAGCTTATGAGAGATGAAC
CTTTTGCTTGCCCTTTATTGGACTCACATGCATTAGCGGACAGTAGTGTCACAGCTAAGAACTTGTCAGTACTTGAAGCT
CAAGGAAACCAGGCAGCACAGGCCAAGGGGCCTAGCCTCTGTGTGGTAAAAGTTATTGAATCTGAGGCACAACAATATCT
TACTGAGCCCAAGAAGTTGACAGAAGTAGTGGAATTTGTCCCAGAAGATGAGATTGAGAGGAACCGTCTGTCACAAGAGG
ACATCCGAAAAATACCTATGTTTGCTTCTTACAGTCCTGGAGAGCCAAACAAAGTACTGTATTTAAAGAACCTTAGTCCT
CGGGTGACTGAGAAGGAACTTGTCTCCTTGTTTGCTAGGTTCCAGGAGGATAAAGGAACTCCAATTCAATTCCGAGTGTT
GACTGGCCGCATGAAGGGCCAGGCCTTCATCACCTTCCCCAGTACGGAGATGGCCCAGCAGGCATTGCTTTTGGTGAATG
GATACAACCTCCTGGGGAAAACACTGGTGATAGAGTTTGGCAAACACAAAAAGCAGAGGGCAGGGCTGCATTTGGCACCC
CCTACCCCACATGTGACACACAACATGACAGAACAAGAT
ORF - retro_mdom_1099 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.65 % |
| Parental protein coverage: | 99.52 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MKRINSSLSSDDLILEDLETEGERQLRSLLHHQLDTSVSVEECVSKKQCFAPAAVYKPFGEEAAGALSLS |
| MKRINSSLSSDDLILEDLETEGERQLRSLLHHQLDTSVSVEECVSKKQCFAPAAVYKPFGEEAAG.LSLS | |
| Retrocopy | MKRINSSLSSDDLILEDLETEGERQLRSLLHHQLDTSVSVEECVSKKQCFAPAAVYKPFGEEAAGVLSLS |
| Parental | QFQALQKSDQEISSLRDLGLNDREIILWKNRASSERGRGLGAAPEATQDRLRDIEEKISEHQRILALPQR |
| QFQALQKSDQEI.SLRDLGL.DREI.LWKNRAS.ERG.GLGA.PEATQD.LRDIEEKISEHQRILALPQR | |
| Retrocopy | QFQALQKSDQEIASLRDLGLTDREIMLWKNRASLERGTGLGATPEATQDCLRDIEEKISEHQRILALPQR |
| Parental | FAGSKQLSRREMEIEKALFQGNDRHSFLRALYYQGESHKRLEAEKDPINNLETVYQEMMAKPHPEEAQLM |
| FAG.KQLSRREMEIEKALFQGNDRHSFLRALYYQGESHKRLEAEKDPINNLETVYQEMMAKPH..EAQLM | |
| Retrocopy | FAGCKQLSRREMEIEKALFQGNDRHSFLRALYYQGESHKRLEAEKDPINNLETVYQEMMAKPHLKEAQLM |
| Parental | RGEPFACPSLDSDVLVDSSGPSKNLSVLEDQGNQAAQAEGSSLHVVKAIESEPQQCLNEPKKLTEVVDFV |
| R.EPFACP.LDS..L.DSS...KNLSVLE.QGNQAAQA.G.SL.VVK.IESE.QQ.L.EPKKLTEVV.FV | |
| Retrocopy | RDEPFACPLLDSHALADSSVTAKNLSVLEAQGNQAAQAKGPSLCVVKVIESEAQQYLTEPKKLTEVVEFV |
| Parental | SEDDIERNRLSEEDIRKIPMFASYSPGEPNKVLYLKNLSPRVTEKELVSLFARFQEKKGPLIQFRVLTGR |
| .ED.IERNRLS.EDIRKIPMFASYSPGEPNKVLYLKNLSPRVTEKELVSLFARFQE.KG..IQFRVLTGR | |
| Retrocopy | PEDEIERNRLSQEDIRKIPMFASYSPGEPNKVLYLKNLSPRVTEKELVSLFARFQEDKGTPIQFRVLTGR |
| Parental | MKGQAFVTFPNMEMAQQALLLVNGYNLLGKTLVIEFGKNKTQMPGLQSASPIPCATDSMTERN |
| MKGQAF.TFP..EMAQQALLLVNGYNLLGKTLVIEFGK.K.Q..GL..A.P.P..T..MTE.. | |
| Retrocopy | MKGQAFITFPSTEMAQQALLLVNGYNLLGKTLVIEFGKHKKQRAGLHLAPPTPHVTHNMTEQD |
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_1099 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1099 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 | ENSMODG00000002312 | 1 retrocopy |
retro_mdom_1099 ,
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