RetrogeneDB ID: | retro_dnov_885 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_11784:14121..15306(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSDNOG00000012291 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MAT1A | ||
| Ensembl ID: | ENSDNOG00000003326 | ||
| Aliases: | None | ||
| Description: | methionine adenosyltransferase I, alpha [Source:HGNC Symbol;Acc:6903] |
Retrocopy-Parental alignment summary:
>retro_dnov_885
ATGAACAGTCAGCTCAACGGCTTCCACGAGGCGTTCATTGAGGAGGGCACATTCCTCTTCACCTCAGAGTCTGTGGGGGA
AGGCCACCCAGATAAGATTTGTGACCAGATCAGTGATGCTGTGCTTGATGCCCACCTTCAGCAGGACCCTGATGCCAAAG
TAGCTTGTGAAACTGTTGCTAAAACTGGAATGATCCTTCTTGCTGGGGAAATTACATCCAGAGCTGCTGTTGACTACCAG
AAAGTGGTTCGTGAAACCATTAAACACATTGGCTATGATGATTCTTCCAAAGGGTTTGACTACAAGACCTGTAATGTGCT
GGTGGCCTTGGAACAACAATCACCAGATATTGCTCAAGGCATTCATCTTGATCGGAATGAGGAAGACATTGGTGCAGGAG
ACCAGGGTTTGATGTTTGGTTAAGCCACTGATGAAACTGAAGAGTGTATGCCTTTAACCATTGTCTTAGCACACAAGCTC
AATGCCAAACTGGCTGAACTACGCCGCAATGGCACTTTGCCTTGGCTACGCCCAGATTCTAAAACTCAAGTGACAGTGCA
GTACATGCAGGATTGAGGTGCTGTGCTTCCCATCAGAGTCCACACAATTCTGATATCGGTTCAGCATGATGAAGATGTTT
GTCTTGATGAGATGAGGGATGCCCTAAAGGAGAAAGTCATCAAAGCTGTTGTACCTGCAAAATGCCTTGATGAGGATACA
ATCTACCACCTTCAGCCAAGTGGCAGATTTGTTATTGGTGGGCCTCAGAGTGATGCTGGTTTGACTGGCCGGAAGATCAT
TGTGGACACTTATGGTGGTTGGGGAACTCACGGAGGAGGTGCCTTTTCAGGAAAGGATTATACCAAGGTGGACCGTTCTG
CTGCTTATGCTGCTCGTTGGGTGGCAAAATCCCTTGTTAAAGGAGGTTTATGCAGAAGGGTTCTTGTTCAGGTCTCTTAT
GCTATTGGAGTTTCTCATCCATTGTCTATCTCCATTTTCCATTATGGCACCTCTCAGAAGAGTGAGAGAGAGCTATTAGA
GATCGTGAAGAAGAATTTTGACCTCCGCCCTGGGGTCATTGTCAGGGATCTGGATCTGAAGAAGCCAATTTATCAGAGGA
CTGCAGCCTATGGCCACTTTGGTAGGGACAGCTTCCCATGGGAAGTGCCCAAAAAGCTTAAATAT
ORF - retro_dnov_885 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.58 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MNGPVDGLCDHSLSEEGAFMFTSESVGEGHPDKICDQISDAVLDAHLRQDPNAKVACETVCKTGMVLLCG |
| MN....G.......EEG.F.FTSESVGEGHPDKICDQISDAVLDAHL.QDP.AKVACETV.KTGM.LL.G | |
| Retrocopy | MNSQLNGFHE-AFIEEGTFLFTSESVGEGHPDKICDQISDAVLDAHLQQDPDAKVACETVAKTGMILLAG |
| Parental | EITSGAMVDYQRVVRDTIQHIGYDDSAKGFDFKTCNVLVALEQQSSDIAQCVHLDRNEEDFGAGDQGLMF |
| EITS.A.VDYQ.VVR.TI.HIGYDDS.KGFD.KTCNVLVALEQQS.DIAQ..HLDRNEED.GAGDQGLMF | |
| Retrocopy | EITSRAAVDYQKVVRETIKHIGYDDSSKGFDYKTCNVLVALEQQSPDIAQGIHLDRNEEDIGAGDQGLMF |
| Parental | GYATDETEECMPLTIILAHKLNARMADLRRSGVLPWLRPDSKTQVTVQYMQDNGAVIPLRIHTIVISVQH |
| G.ATDETEECMPLTI.LAHKLNA..A.LRR.G.LPWLRPDSKTQVTVQYMQD.GAV.P.R.HTI.ISVQH | |
| Retrocopy | G*ATDETEECMPLTIVLAHKLNAKLAELRRNGTLPWLRPDSKTQVTVQYMQD*GAVLPIRVHTILISVQH |
| Parental | DEDIDLEGMRTALKEQVIRAVVPAKYLDEDTIYHLQPSGRFVIGGPQGDAGVTGRKIIVDTYGGWGAHGG |
| DED..L..MR.ALKE.VI.AVVPAK.LDEDTIYHLQPSGRFVIGGPQ.DAG.TGRKIIVDTYGGWG.HGG | |
| Retrocopy | DEDVCLDEMRDALKEKVIKAVVPAKCLDEDTIYHLQPSGRFVIGGPQSDAGLTGRKIIVDTYGGWGTHGG |
| Parental | GAFSGKDYTKVDRSAAYAARWVAKSLVKAGLCRRVLVQVSYAIGVAEPLSISIFTYGTSRKTERELLDIV |
| GAFSGKDYTKVDRSAAYAARWVAKSLVK.GLCRRVLVQVSYAIGV..PLSISIF.YGTS.K.ERELL.IV | |
| Retrocopy | GAFSGKDYTKVDRSAAYAARWVAKSLVKGGLCRRVLVQVSYAIGVSHPLSISIFHYGTSQKSERELLEIV |
| Parental | NKNFDLRPGVIVRDLDLKKPIYQKTACYGHFGRSEFQ-EVPKRLVF |
| .KNFDLRPGVIVRDLDLKKPIYQ.TA.YGHFGR..F..EVPK.L.. | |
| Retrocopy | KKNFDLRPGVIVRDLDLKKPIYQRTAAYGHFGRDSFPWEVPKKLKY |
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 | 45 .51 RPM | 0 .58 RPM |
| SRP012922_cerebellum | 44 .13 RPM | 0 .41 RPM |
| SRP012922_heart | 12 .99 RPM | 0 .23 RPM |
| SRP012922_kidney | 39 .70 RPM | 14 .78 RPM |
| SRP012922_liver | 8 .36 RPM | 1175 .60 RPM |
| SRP012922_lung | 49 .94 RPM | 0 .92 RPM |
| SRP012922_quadricep_muscle | 15 .75 RPM | 0 .35 RPM |
| SRP012922_spleen | 54 .14 RPM | 0 .11 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_885 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 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000003326 | 2 retrocopies |
retro_dnov_799, retro_dnov_885 ,
|
| Tarsius syrichta | ENSTSYG00000000972 | 1 retrocopy |