RetrogeneDB ID: | retro_mdom_1466 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 5:181862024..181862574(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMODG00000024819 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | AKIRIN1 | ||
| Ensembl ID: | ENSMODG00000017703 | ||
| Aliases: | None | ||
| Description: | akirin 1 [Source:HGNC Symbol;Acc:25744] |
Retrocopy-Parental alignment summary:
>retro_mdom_1466
ATGGCGTGCGGGATGATGCTGAAGCAACCCATGGAGTTTGAGGTGGCACTTCTAAGCCCCAGCTCGCTGGCACGGCTCCC
CCTTGCTGGACCCTGCACCTTGCCTGCAGCCCCCAGACACTGAACCGCTGCCTCAGCCTCAGCTCCAGCCCCTGCCGCAG
TCGCCCAGCAGCAAGCGCCACCTGAGGACCCTGGAGCAAATATTTCACAACATCAAACAAGAATACAGTTGCTATCACAG
GTGGAGACAATTAGAAGCTGTCCTTAATCAGAGTGAAACCTGCACTTCAGAGGGTCAGTCACCTTCTTTAGGTCTTACAG
CACCATGTTCACCAAGTTCATCCTGGATGAAAAAGGACCAGCCGACATTTACATTTTGCCAAGTGAGACTATTGTGTGAA
AGCCTTTTAAAAGACTATGAAGATAGGATTCAGGAGGAATATGAGCAAATCCTCAATACAAAATTAGCAGAACAATATGA
ATCTTTTGTGAAATTCACACATGATCATATCATGTGAAGCTATGGGACAAGGCCAACAAGCTATGTGTCT
ORF - retro_mdom_1466 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.72 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MACGATLKRPMEFEAALLSPGSPKRRRCAPLPG-PAPGLRPPDTEPPPQPQLQPPPPSPPGSERRLRTPE |
| MACG..LK.PMEFE.ALLSP.S..R....PL.G.PAP.L.PPDTEP.PQPQLQP.P.S.P.S.R.LRT.E | |
| Retrocopy | MACGMMLKQPMEFEVALLSPSSLAR---LPLAG>PAPCLQPPDTEPLPQPQLQPLPQS-PSSKRHLRTLE |
| Parental | QIFQNIKQEYSRYQRWRQLEVVLNQSEACTSEGQSHSSGLTAPSSPGSSWMKKDQPTFTLRQVGLLCERL |
| QIF.NIKQEYS.Y.RWRQLE.VLNQSE.CTSEGQS.S.GLTAP.SP.SSWMKKDQPTFT..QV.LLCE.L | |
| Retrocopy | QIFHNIKQEYSCYHRWRQLEAVLNQSETCTSEGQSPSLGLTAPCSPSSSWMKKDQPTFTFCQVRLLCESL |
| Parental | LKDYEDRIREEYEQILNTKLAEQYESFVKFTHDQIMRRYGTRPTSYVS |
| LKDYEDRI.EEYEQILNTKLAEQYESFVKFTHD.IM..YGTRPTSYVS | |
| Retrocopy | LKDYEDRIQEEYEQILNTKLAEQYESFVKFTHDHIM*SYGTRPTSYVS |
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_1466 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1466 was not experimentally validated.