RetrogeneDB ID: | retro_mdom_545 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 1:257316934..257317348(-) | ||
| Located in intron of: | ENSMODG00000007703 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSMODG00000009520 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_mdom_545
ATTTTCACCTGAGCCAAGCTTGCCTGCTTGATCCGTGCTGGATCCAGAATTGTATACAGATCAATTTCTTCAGCAGTGTT
GTCTCGACAAAAGGTCAGGCCTGGAGAGGGCAACACAGTATCTAATGGGACCCAGAACAGGGTGTCTCAGCTAGCATTAA
GGGAATTCCAAACCAGTGCTATCAGAAGAGATGTTGATACTGCTGCTAAATTTATTGGTGCAGGTGCTGCCACAGTATGA
GTGGTTGGTTCTGATGCTGGTATTGGAACTATCTTTGGTTCTCTCATTATTGGTTATGCCAGAAACCCATCACTGAAGCA
GCAGCTGTTCTCATATGCTATCCTGGAATTCACCTTGTCTGAAGCTATGGGTCTCTTTTGTTTGATGGTTGCTTTCTTGA
TCTTGTTTGCCATG
ORF - retro_mdom_545 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.82 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MFACAKLACSPALIRAGSRIVYRPISAAVLSRPEVRTGEGNTVSNGAQNRVSQLALREFQTSAISRDVDT |
| .F..AKLAC...LIRAGSRIVYR.IS.AVLSR..VR.GEGNTVSNG.QNRVSQLALREFQTSAI.RDVDT | |
| Retrocopy | IFT*AKLAC---LIRAGSRIVYRSISSAVLSRQKVRPGEGNTVSNGTQNRVSQLALREFQTSAIRRDVDT |
| Parental | AAKFIGAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMVAFLILFA |
| AAKFIGAGAATV.V.GS.AGIGT.FGSLIIGYARNPSLKQQLFSYAIL.F.LSEAMGLFCLMVAFLILFA | |
| Retrocopy | AAKFIGAGAATV*VVGSDAGIGTIFGSLIIGYARNPSLKQQLFSYAILEFTLSEAMGLFCLMVAFLILFA |
| Parental | L |
| . | |
| Retrocopy | M |
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 .95 RPM | 0 .00 RPM |
| SRP007412_cerebellum | 1 .31 RPM | 0 .00 RPM |
| SRP007412_heart | 0 .20 RPM | 0 .00 RPM |
| SRP007412_kidney | 1 .32 RPM | 0 .00 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .00 RPM |
| SRP007412_testis | 0 .79 RPM | 0 .00 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_545 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_545 was not experimentally validated.