RetrogeneDB ID: | retro_dnov_533 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | GeneScaffold_5853:295487..296117(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MED20 | ||
| Ensembl ID: | ENSDNOG00000016666 | ||
| Aliases: | None | ||
| Description: | mediator complex subunit 20 [Source:HGNC Symbol;Acc:16840] |
Retrocopy-Parental alignment summary:
>retro_dnov_533
TTGGGAGGGACTTGTGTGTCCCAGATGCCTGTGGCTGAGGGCAAGAGTGTCCAGCAGACTGTGGAGCACCTTATCCGGAA
GTTGGAGATGCTTGGAACAGAGGAACAAGGAACATTTTGTGTGGACTGTGAGACCTGCTATACAGCTGGTTCCACCCTTG
GCAGCCAAGGTCAGGCCAGGAAGCTGATGTATGTGATGCACTCAGGGTACTCTTTGAGCTGCTTTGCCCTCTTTGAGAAT
GGACATTGCCTTATTGCTGATACCAACTTTGATGTGCTTATGGTGAAGCTCAAGGGTTTTGTCCAGAGTGCCAAGGCCAG
CAAGATGGAGACCCGGGGTACCCGTCACCAGTGCTGTGACTTCCTAGTGAAGGTGGGCACAGTCACAATGGGACCCAGCA
CCCGGGGCATCTCTGTGGAGGTGGAGTATGGCCCGTGTGTGGTACCCAGTGGCTGCTGGAGCCTGCTACTTGAGTTCCTA
CAGAGTTTTTTGGGTACCCACACACCAGGGCCTCCTGCAGTGTTTGGGAATAGACATGATGCAATATATGGCCCAGCAGA
TACCATGATCCAGTACATGGAATTGTTCAACAAGATCCGCAACCAGCAGCAGGTGCTGGTGGCTGGGATT
ORF - retro_dnov_533 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.04 % |
| Parental protein coverage: | 99.53 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MGVTCVSQMPVAEGKSVQQTVELLTRKLEMLGAEKQGTFCVDCETFHTAASTLGSQGQAGKLMYVMHNSE |
| .G.TCVSQMPVAEGKSVQQTVE.L.RKLEMLG.E.QGTFCVDCET..TA.STLGSQGQA.KLMYVMH.S. | |
| Retrocopy | LGGTCVSQMPVAEGKSVQQTVEHLIRKLEMLGTEEQGTFCVDCETCYTAGSTLGSQGQARKLMYVMH-SG |
| Parental | YPLSCFALFENGPCLIADTNFDVLMVKLKGFFQSAKASKIETRGTRYQYCDFLVKVGTVTMGPSARGISV |
| Y.LSCFALFENG.CLIADTNFDVLMVKLKGF.QSAKASK.ETRGTR.Q.CDFLVKVGTVTMGPS.RGISV | |
| Retrocopy | YSLSCFALFENGHCLIADTNFDVLMVKLKGFVQSAKASKMETRGTRHQCCDFLVKVGTVTMGPSTRGISV |
| Parental | EVEYGPCVVASDCWSLLLEFLQSFLGTXXXXXXXXXXSRHDAVYGPADTMVQYMEC-HKIRKQQQVPVAE |
| EVEYGPCVV.S.CWSLLLEFLQSFLGT...........RHDA.YGPADTM.QYME...KIR.QQQV.VA. | |
| Retrocopy | EVEYGPCVVPSGCWSLLLEFLQSFLGTHTPGPPAVFGNRHDAIYGPADTMIQYMELFNKIRNQQQVLVAG |
| Parental | I |
| I | |
| Retrocopy | I |
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 |
|---|---|---|
| SRP012922_ascending_colon | 0 .78 RPM | 19 .84 RPM |
| SRP012922_cerebellum | 0 .27 RPM | 10 .72 RPM |
| SRP012922_heart | 0 .93 RPM | 5 .80 RPM |
| SRP012922_kidney | 0 .27 RPM | 13 .14 RPM |
| SRP012922_liver | 0 .15 RPM | 8 .82 RPM |
| SRP012922_lung | 0 .46 RPM | 14 .20 RPM |
| SRP012922_quadricep_muscle | 0 .17 RPM | 6 .06 RPM |
| SRP012922_spleen | 0 .80 RPM | 18 .89 RPM |
Dasypus novemcinctus was not studied using ChIP-Seq data.
Dasypus novemcinctus was not studied using EST data.
Dasypus novemcinctus was not studied using FANTOM5 data.
retro_dnov_533 was not experimentally validated.
Retrocopy orthology:
Dasypus novemcinctus 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 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000001613 | 1 retrocopy | |
| Dasypus novemcinctus | ENSDNOG00000016666 | 1 retrocopy |
retro_dnov_533 ,
|
| Microcebus murinus | ENSMICG00000011326 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000014024 | 1 retrocopy |