RetrogeneDB ID: | retro_mdom_1851 | ||
Retrocopylocation | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 8:97164474..97164953(+) | ||
| Located in intron of: | ENSMODG00000017771 | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | TLCD1 | ||
| Ensembl ID: | ENSMODG00000019299 | ||
| Aliases: | None | ||
| Description: | TLC domain containing 1 [Source:HGNC Symbol;Acc:25177] |
Retrocopy-Parental alignment summary:
>retro_mdom_1851
CTCTGGCAGACTCCAGAGGTTCTGGTGGAGGTTGAGATTGCATCTTTTCTCTCTGGGTGTTTCTGCGTCTGCTTCTCTGC
TGGCTGTTTTATCCATGACACATTGGGCATCATGGTGAACAAGCAGGCTAGGGCGTCTTGGGAACATTTGGCCCATCACA
TCTTGGCCATCTTTGCCTTTGTCTCGGTCACCTTTAAGAGCTGCTTCATGACAGGTGGGGTCCTGACCTTCTTTGTGAAA
GTCAGCAACAACTTCCTTATGAAAAGATGATGATGAAGTTCAGCAACCATCAGGACAGTGTTTTCCACAAAGTCAATAAA
CACATCAACCTGGTCATGTACTATCTACGCCACCCCCACCTCCCTGCCTACCTCATCACCTTTTTCCTTTATTATCCTGG
CCAGAGGACATGGGGACCCTGTAGGCTCAGCATCCTGATGATGCTGGATTTGATGGTTCTCATCAATTTTCCCCACCTC
CTCTGGCAGACTCCAGAGGTTCTGGTGGAGGTTGAGATTGCATCTTTTCTCTCTGGGTGTTTCTGCGTCTGCTTCTCTGC
TGGCTGTTTTATCCATGACACATTGGGCATCATGGTGAACAAGCAGGCTAGGGCGTCTTGGGAACATTTGGCCCATCACA
TCTTGGCCATCTTTGCCTTTGTCTCGGTCACCTTTAAGAGCTGCTTCATGACAGGTGGGGTCCTGACCTTCTTTGTGAAA
GTCAGCAACAACTTCCTTATGAAAAGATGATGATGAAGTTCAGCAACCATCAGGACAGTGTTTTCCACAAAGTCAATAAA
CACATCAACCTGGTCATGTACTATCTACGCCACCCCCACCTCCCTGCCTACCTCATCACCTTTTTCCTTTATTATCCTGG
CCAGAGGACATGGGGACCCTGTAGGCTCAGCATCCTGATGATGCTGGATTTGATGGTTCTCATCAATTTTCCCCACCTC
ORF - retro_mdom_1851 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 60.25 % |
| Parental protein coverage: | 64.78 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | VWETPEMLVEIETASSLSGYFLVCFSTGYFIHDSLDIVLNKQAQASWEYLLHHVLAIFAFSSGVFKGSFV |
| .W.TPE.LVE.E.AS.LSG.F.VCFS.G.FIHD.L.I..NKQA.ASWE.L.HH.LAIFAF.S..FK..F. | |
| Retrocopy | LWQTPEVLVEVEIASFLSGCFCVCFSAGCFIHDTLGIMVNKQARASWEHLAHHILAIFAFVSVTFKSCFM |
| Parental | AGGVLILLVEISNIFLTIR-MMLKLSNHQDSVFYKINKYINLVMYFLFRVAPQAYLTMYFLRYLGQRTQG |
| .GGVL...V..SN.FL..R.MM.K.SNHQDSVF.K.NK.INLVMY.L......AYL...FL.Y.GQRT.G | |
| Retrocopy | TGGVLTFFVKVSNNFLMKR<MMMKFSNHQDSVFHKVNKHINLVMYYLRHPHLPAYLITFFLYYPGQRTWG |
| Parental | AFLLGILLMVDMMILVYFSRL |
| ...L.IL.M.D.M.L..F..L | |
| Retrocopy | PCRLSILMMLDLMVLINFPHL |
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_1851 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1851 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 | ENSMODG00000019299 | 1 retrocopy |
retro_mdom_1851 ,
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