RetrogeneDB ID: | retro_mdom_1459 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 5:152860278..152860667(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PSMB4 | ||
| Ensembl ID: | ENSMODG00000018871 | ||
| Aliases: | None | ||
| Description: | proteasome (prosome, macropain) subunit, beta type, 4 [Source:HGNC Symbol;Acc:9541] |
Retrocopy-Parental alignment summary:
>retro_mdom_1459
ATATCTCAAATCATGCCTGTCAACTATTACATGTTTGGTACTTCTGGGGATTATTCTGATTTTCAGTACATGAAGCAAGT
CATTGACCAGATGGTTACTAATGAAGAGCTGATGAGTGATGAATATAGCTGTAGCCCCAAAGCTATCTACTCTTGGTTGA
CCAGAGTTATATATATTTGTTTCTCCAAGATGAACTCCCTCTAAAACATGATAGTCATTGTTGGATTTTAGGATGTGAAG
AACTTCCTTGGTTATGTGGACATACTTAGTGTATCCTATGAAGTCACCATGCTGGTTCCTAGTTATGATGTCTATTGGCC
CAGTCCTTGATGAAAGAGCTTTTGAAAAAGCCAATTCTAATCCATACAAAATCATGTGAGTTAGTGGAG
ORF - retro_mdom_1459 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 56.82 % |
| Parental protein coverage: | 58.22 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | ISRIMRVNNNTMLGASGDYADFQYVKQVIDQMVIDEELLGDGHSYSPKAIHSWLTRAMYSRRSKMNPLWN |
| IS.IM.VN...M.G.SGDY.DFQY.KQVIDQMV..EEL..D..S.SPKAI.SWLTR..Y...SKMN.L.N | |
| Retrocopy | ISQIMPVNYY-MFGTSGDYSDFQYMKQVIDQMVTNEELMSDEYSCSPKAIYSWLTRVIYICFSKMNSL*N |
| Parental | TMVIGGYADGESFLGYVDMLGVAYEAPTLATGYGAY-LAQPLMREVLEKKQFKQAEARELVE |
| ..VI.G..D...FLGYVD.L.V.YE...L...Y..Y.LAQ.LM.E.L.K.........ELVE | |
| Retrocopy | MIVIVGF*DVKNFLGYVDILSVSYEVTMLVPSYDVY<LAQSLMKELLKKPILIHTKSCELVE |
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_1459 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1459 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 | |
|---|---|---|---|
| Microcebus murinus | ENSMICG00000016746 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000018871 | 1 retrocopy |
retro_mdom_1459 ,
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