RetrogeneDB ID: | retro_mdom_1152 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 3:261046869..261047252(-) | ||
| Located in intron of: | ENSMODG00000021499 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ICT1 | ||
| Ensembl ID: | ENSMODG00000007126 | ||
| Aliases: | None | ||
| Description: | immature colon carcinoma transcript 1 [Source:HGNC Symbol;Acc:5359] |
Retrocopy-Parental alignment summary:
>retro_mdom_1152
CTATCTTATTCCAAAAGCGGAGGCCCTGAAGACAGAATGTTAAAGAAGTAAATATCAAGGCTGAAGTGCAGTTCCATTTA
ACAACAGCAGACTGGATTACAGAGCCTGTCTGACAAAAGATTGAAAACTTGTTCAAAAACAAGATCTGCAAATCAGGAGA
GCTGACCATCATCTCTGACTCCTGCCTTTATCAGTTTTGAAGTTTGGCAGATTGCCTCCAGAATATCTGAGACATGATTG
CCCAGGCTAGCCAAGTTCCCAAGGAGCTGTCCAAAGAAGATGCTGGGCTTTGAAGACTCAGGGTAGAAATCATGAATCAT
GAAAAGCTAAGACAGAAGAGAATCCATTCTTCCATAAACACAAGCAAGAAAGAAGATACTGAC
ORF - retro_mdom_1152 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 69.77 % |
| Parental protein coverage: | 61.54 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | VSYSKSSGPGG-QNVNKVNTKAEVRFHLATADWIAEPVRQKISVLFKNKISKSGELIITSDSSRYQFRNL |
| .SYSKS.GP...QNV..VN.KAEV.FHL.TADWI.EPV.QKI..LFKNKI.KSGEL.I.SDS..YQF..L | |
| Retrocopy | LSYSKSGGPED<QNVKEVNIKAEVQFHLTTADWITEPV*QKIENLFKNKICKSGELTIISDSCLYQF*SL |
| Parental | ADCLQKIRDMIAQASQVPKEPSKEDAVLRRIRIENSNRERLRQKRIHSSTKANRKIDMD |
| ADCLQ.I.DMIAQASQVPKE.SKEDA.L.R.R.E..N.E.LRQKRIHSS.....K.D.D | |
| Retrocopy | ADCLQNI*DMIAQASQVPKELSKEDAGL*RLRVEIMNHEKLRQKRIHSSINTSKKEDTD |
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_1152 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1152 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 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dipodomys ordii | ENSDORG00000006439 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000011644 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000007126 | 1 retrocopy |
retro_mdom_1152 ,
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