RetrogeneDB ID: | retro_mdom_1101 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 3:109804282..109804804(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSMODG00000002844 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_mdom_1101
AGGAGAGAAACATAGGAAAAGAACTTGAAAATGATTTAAATGCACAGTCTGGAGTACAGCATGGACAAACATAGTTTCCA
GATGGGAATGAACAAGTTTGGTGACATGACCACTGAAGAATTCAAACAAATGATGAATGGCTATAAGTCCAATAGATCAG
AGAGGAGGACCAAAGGATCTCTGTTTCATGAAGCTCTCTTTGCACAGATTCCTGCATATGTAGATTGGAGAGAAAAAGGC
ATTGTAACTCATTTTAATGGTCAGAGTCAGTATGGTTCTTGTTGGGCATTTAGTGCCACTGGCTCCCTTGAAGATAAGTG
GTTCCATAAAAAAAGGCAAACTTGTTTCACTTAGTGAATAGAACTTGGTTGACTGCTCTTCTTCTGAAAGCAATGGCTAT
TGTGTTGTTTTCATGGACAAAGTCTTCCAATATGTGAAGAAAATGGTGGCATTGATACAGAAGAATGCTATCCATATGTT
GAAGAGCATAACAAATGCAAATATCAGTCAGAAAACTCTGGT
ORF - retro_mdom_1101 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 62.15 % |
| Parental protein coverage: | 52.55 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | RRATWEKNLKMIERHNQEYSAGKHSFQLRMNKFGDMTTEEFQEAINFYNSSASQRRTKRYLHREPLLAQL |
| RR.T.EKNLKMI..H..EYS..KHSFQ..MNKFGDMTTEEF....N.Y.S..S.RRTK..L..E.L.AQ. | |
| Retrocopy | RRET*EKNLKMI*MHSLEYSMDKHSFQMGMNKFGDMTTEEFKQMMNGYKSNRSERRTKGSLFHEALFAQI |
| Parental | PESVDWREEGYVTPVKNQGQCLSCWAFSAVGAIEGQWFR-KTGELVSLSIQNLVDCTTSDSISSCHGGFM |
| P..VDWRE.G.VT....Q.Q..SCWAFSA.G..E..WF..K.G.LVSLS..NLVDC..S.S...C...FM | |
| Retrocopy | PAYVDWREKGIVTHFNGQSQYGSCWAFSATGSLEDKWFH>KKGKLVSLSE*NLVDCSSSESNGYC-VVFM |
| Parental | DRAFQYV-QDNGGIDTEECYPYVGEVNECKYQPECSG |
| D..FQYV...NGGIDTEECYPYV.E.N.CKYQ.E.SG | |
| Retrocopy | DKVFQYV<EENGGIDTEECYPYVEEHNKCKYQSENSG |
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_1101 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1101 was not experimentally validated.