RetrogeneDB ID: | retro_mdom_1538 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 5:157704610..157705075(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ARF4 | ||
| Ensembl ID: | ENSMODG00000000185 | ||
| Aliases: | None | ||
| Description: | ADP-ribosylation factor 4 [Source:HGNC Symbol;Acc:655] |
Retrocopy-Parental alignment summary:
>retro_mdom_1538
ATTCTAATGGTTGGTCTGGATGTTACAGGAAAACCAAATATTTTGAACAAACTAAAGCTAGGTGAATTAGTCATTGCTAT
TTCCACTATAGGGTTCAACATATAAACTGCAGAATATAAAAACAGCTCCACAGTGTGGAATGTAGGTAGCCTGGACAATA
TCTGACTTCTATGGCACCATAATTTCTAGAAAAAACAAGAACTGATATTTGAGCTTGACAGTAATGACAGAAAACCAATG
AATGAGTCCCAACAACATCTAATGAGAAGTTGGCAGAGGATAATCTGAGATGCTGTCTTAGTGTCTGCTAACAAATATGA
TCTCCTCAATGCTACAAATACATCTGAAATCACAGATAAACTTAAATTGCATTCTCTTCATCACAGAAGCTGGTACATCT
ATGCCATCTGTTCCATTAGAGGGTATGGACTCTCTGAAGGATTAGACTAGTTGTCCCATCAGCTC
ORF - retro_mdom_1538 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 55.06 % |
| Parental protein coverage: | 87.78 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNICFTVWDVGGQDKIRPLWRHYFQNTQGLI |
| ILMVGLD..GK..IL.KLKLGE.V..I.TIGFN..T.EYKN...TVW.VG..D.I..LW.H.F...Q.LI | |
| Retrocopy | ILMVGLDVTGKPNILNKLKLGELVIAISTIGFNI*TAEYKN-SSTVWNVGSLDNI*LLWHHNF*KKQELI |
| Parental | FVVDSNDRERIQEGAEELQKMLQEDELRDAVLLLFANKQDLPNAMAISEMTDKLGLQSLRNRTWYVQATC |
| F..DSNDR....E....L....Q.....DAVL...ANK.DL.NA...SE.TDKL.L.SL..R.WY..A.C | |
| Retrocopy | FELDSNDRKPMNESQQHLMRSWQR-II*DAVL-VSANKYDLLNATNTSEITDKLKLHSLHHRSWYIYAIC |
| Parental | ATQGTGLYEGLDWLSNEL |
| ...G.GL.EGLD.LS..L | |
| Retrocopy | SIRGYGLSEGLD*LSHQL |
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_1538 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1538 was not experimentally validated.