RetrogeneDB ID: | retro_mdom_567 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 1:325331689..325332202(-) | ||
| Located in intron of: | ENSMODG00000012835 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SYNDIG1L | ||
| Ensembl ID: | ENSMODG00000024016 | ||
| Aliases: | None | ||
| Description: | synapse differentiation inducing 1-like [Source:HGNC Symbol;Acc:32388] |
Retrocopy-Parental alignment summary:
>retro_mdom_567
ATGCAACTAGCTATAGAGGCACTGTATGAGTCCATCTTTCCCCCTGATGAAGGACAAAGCAAAAGAGTGTAAAGGTGATA
ACCATGGAACTAACTTCACAGAGAGCAAGGAGCTCCAGGCCAGCACCACTGAAGGAGTCCAGAGACCCAGCTAGGCTGAG
GAAGATGCCATTATTCAGACAATATGCTTTGAAGTAGAAAAGGAGTTTCTAGAGTTGGAAGAAGATGATAATGATGAGAG
TGATTCTTTCAAAGCCAGTGAGAGTGAAGATGTTTTCCTTATCTACCACCCTGGGACCACCTTGGCCTCACCATCTTCTC
CATGCTTTCTGTTCCATGGCCCCTGGGCATTGCTGCCTTCTACTTTTTACAAAGGACAAGCAAGGCAATCTCCAAAGGGG
ACTTTTGCCTGGCCAGCATGACTTCCTGACAGGCCCTTTTCCTGGCCATCCTTTTCATCACCACTGGCACCCATGTCAAT
GTTGCAGTGGTGGTGGCACTGGTGACTTACTTG
ORF - retro_mdom_567 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.99 % |
| Parental protein coverage: | 72.46 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | LQLAVEALYGS-NFLLVKDKAKEWKGDSCETTFTESKEPQASTPERVQRPGEAEEDAKIQTVSFEVEEEF |
| .QLA.EALY.S..F.L.KDKAKE.KGD...T.FTESKE.QAST.E.VQRP..AEEDA.IQT..FEVE.EF | |
| Retrocopy | MQLAIEALYES>SFPLMKDKAKECKGDNHGTNFTESKELQASTTEGVQRPS*AEEDAIIQTICFEVEKEF |
| Parental | LEVEEEDDDESDSSSASESEDGFLT-LPPRDHLGLAIFSMLCCFWPLGIAAFYFSQRTSKAISKGDFHLA |
| LE.EE.D.DESDS..ASESED.FL..LPP.DHLGL.IFSML...WPLGIAAFYF.QRTSKAISKGDF.LA | |
| Retrocopy | LELEEDDNDESDSFKASESEDVFLI<LPPWDHLGLTIFSMLSVPWPLGIAAFYFLQRTSKAISKGDFCLA |
| Parental | SMTSRRAFFLAILSITIGTGVYIAVVVALVAYL |
| SMTS..A.FLAIL.IT.GT.V..AVVVALV.YL | |
| Retrocopy | SMTS*QALFLAILFITTGTHVNVAVVVALVTYL |
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 | 50 .42 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 17 .63 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 | 6 .68 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_567 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_567 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 | ENSMODG00000024016 | 1 retrocopy |
retro_mdom_567 ,
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