RetrogeneDB ID: | retro_mdom_329 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 1:154363292..154364093(+) | ||
| Located in intron of: | ENSMODG00000009566 | ||
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_329
GAAGACAACTGGGAAAAGAACTTAAAAAGCAAGATAAGTCATCTGGAAACAGAAAACAGTGTCTTGAAAGCCAAGATTAA
TCAACCTGAAAATGAGGCAACAAAGATGAAAGATGACCTCAAAAGAAAATCAGACCAGAAGGAAAAGGATGACCAAAAAG
CCAAGGATAAAATGCAGTCTTTAAAAACCAGAATACAACAATCAGAAGCAAATGACTTCACAAGGCAGCAGGACACTATA
AAACAAAATGAAAAGAATGAAAAAATTGAGGAAAATATGAAGTATCTCATTCACAAAACAGAAGATTTAGAAAATAGTTC
TACAAGAGATAAATTAAGAATCATTGGTCTACTGGAAGACCATGACAAAAGAAAATCCTGGACATGATACTACAGGAAAT
TATTCAAGAAAACTGCCCCGATATTCTAGGAAAAGAGGGAAAAGTGGAGACTGAAAGTCCCCAACTGACAACACTCAGGA
ATGTTATAGATAAATTCATGAACTATCAGACCAAGGAAAAAATATTACAAGATGCCAAGAAGAAGTCATTCAGATACCAT
GGAACCACAGTGAGGATAACACAGGATCTGGCTGCATCTACACTGAAAAGACCAAAAGTCATGGAATATGATATTCTGTA
AAGCAAGGGAACTAGGTCTACAACCAAAAATCAATTACCCAGCAAAATTGACTATAATCTTACAGAGGAAAGTATGGTCA
TCTAACAAAATACAATAATTGCAAGCATTTGTAAATAAAAGACCAGATGTGAACCTAAAATCTGATGCCCAAACACAGAA
C
ORF - retro_mdom_329 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 63.57 % |
| Parental protein coverage: | 77.35 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | EDQTEKQKQS----LKTRIKQLEDKQEKHEKVNTKHRETEKRISDQKEKDDEKARDEIQSFKTRIQQLEA |
| ED..EK...S....L.T....L..K....E...TK.....KR.SDQKEKDD.KA.D..QS.KTRIQQ.EA | |
| Retrocopy | EDNWEKNLKSKISHLETENSVLKAKINQPENEATKMKDDLKRKSDQKEKDDQKAKDKMQSLKTRIQQSEA |
| Parental | SDFTRHQHTIKQNQKNKIIEENMKHLIHKTEDLENRSRRDNLRIIGLLEDYDKRKS-LDIILQEIIQENC |
| .DFTR.Q.T.............MK.LIHKTEDLEN.S.RD.LRIIGLLED.DKRKS.LD.ILQEIIQENC | |
| Retrocopy | NDFTRQQDTXXXXXXXXXXXXXMKYLIHKTEDLENSSTRDKLRIIGLLEDHDKRKS<LDMILQEIIQENC |
| Parental | PDITEQEGKVEIERIHRSTHRNVLAKFKKSQTKEKILQVDKKKSFRKHGTIVRITQDLTASTL-KDLQAW |
| PDI...EGKVE.E.....T.RNV..KF...QTKEKILQ..KKKSFR.HGT.VRITQDL.ASTL.KD...W | |
| Retrocopy | PDILGKEGKVETESPQLTTLRNVIDKFMNYQTKEKILQDAKKKSFRYHGTTVRITQDLAASTL>KDQKSW |
| Parental | NMIFWKARELGLQPRIIYTAKLTIFLQGKVWSFNKIEDFQAFVKKRPDMNRKFDAEAQN |
| NMIF.KARELGLQP.I.Y.AKLTI.LQ.KVWS.NKI...QAFV.KRPD.N.K.DA..QN | |
| Retrocopy | NMIFCKARELGLQPKINYPAKLTIILQRKVWSSNKIQ*LQAFVNKRPDVNLKSDAQTQN |
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 .24 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 .59 RPM | 0 .00 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_329 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_329 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 ,
|