RetrogeneDB ID: | retro_mdom_1477 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 5:223359284..223360053(+) | ||
| 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: | ENSMODG00000002633 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_mdom_1477
GAAAAAGAGACACATGAACTAAAAGAAGAAAATAGTGTCTTGAAAGCTAGAATTGACCAGCTTGAAAACAAGGCAAAGAT
GATGAAAGATGACTTACAAAGAAAATCAGACCAGAAGAAGGATGACCAAAAATTCAGGAATGAAATTCTGTCTTTAAAAA
TTAGGATCCAACAACTAGAAGCAAATGACTTCACAAAGCAGCAAGGATCTATAAAACAAAATCAAAAGAATGAAAAAATT
GAGGAAAATATGAAATATCTCATTGACAAAAATGTCAGACCATGAAAACAGATTCAGAAGAGAGAATTTAAAAATTATTG
GACTACTGGAAGATCATGATAAAAGAAAAAACCTGGATATCATTCTACAGGAAATTATCCAAGAAAACTGCCCTGACATT
CTAGAGCAAGAGGGAAAAGTGGAGATTGAAGGAATCCACATATCACCTTCTATACTTAATGTTATAGCCAAATTCAAGAA
CTATCAGACCAAGGGAAAAATATTACAAGCTTCTAAGAAGAAGTCATTCAGATACCATGGAACCGCAGTTAGGATAACAC
AGGCTGCATCTACACTGAAGGACTGAAAGGCATGGAATACGATTTTCCAGAAAACAATGGAATTGGGTCTACAACCAAGA
ATCAACTACCCAGCAAAACTGACTATATTCTTACAGGGGAAAGTATGGTCATTTAATAAATCAGAATACTTCCAAGCATT
CATAGAGAAAATACAAGACTTAAACAGAAAATTTGATGCCCAGAACCAA
ORF - retro_mdom_1477 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 61.15 % |
| Parental protein coverage: | 75.88 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | EKQKQSLKTRIKQLEDKQEKHEKVNTKHRETEKRISDQKEKDDEKARDEIQSFKTRIQQLEASDFTRHQH |
| EK....LK.....L.......E...........R.SDQK.KDD.K.R.EI.S.K.RIQQLEA.DFT..Q. | |
| Retrocopy | EKETHELKEENSVLKARIDQLENKAKMMKDDLQRKSDQK-KDDQKFRNEILSLKIRIQQLEANDFTKQQG |
| Parental | TIKQNQKNKIIEENMKHLIHKT-EDLENRSRRDNLRIIGLLEDYDKRKSLDIILQEIIQENCPDITEQEG |
| .................LI.K...D.ENR.RR.NL.IIGLLED.DKRK.LDIILQEIIQENCPDI.EQEG | |
| Retrocopy | SXXXXXXXXXXXXXXXXLIDKN>SDHENRFRRENLKIIGLLEDHDKRKNLDIILQEIIQENCPDILEQEG |
| Parental | KVEIERIHRS-THRNVLAKFKKSQTKEKILQVDKKKSFRKHGTIVRITQDLTASTLKDLQAWNMIFWKAR |
| KVEIE.IH.S....NV.AKFK..QTK.KILQ..KKKSFR.HGT.VRITQ...ASTLKD..AWN.IF.K.. | |
| Retrocopy | KVEIEGIHISPSILNVIAKFKNYQTKGKILQASKKKSFRYHGTAVRITQ--AASTLKD*KAWNTIFQKTM |
| Parental | ELGLQPRIIYTAKLTIFLQGKVWSFNKIEDFQAFVKKRPDMNRKFDAEAQ |
| ELGLQPRI.Y.AKLTIFLQGKVWSFNK.E.FQAF..K..D.NRKFDA..Q | |
| Retrocopy | ELGLQPRINYPAKLTIFLQGKVWSFNKSEYFQAFIEKIQDLNRKFDAQNQ |
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_1477 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1477 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 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000002633 | 6 retrocopies |
retro_mdom_1009, retro_mdom_1362, retro_mdom_1477 , retro_mdom_1723, retro_mdom_1764, retro_mdom_329,
|