RetrogeneDB ID: | retro_dnov_799 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_108891:6261..7348(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
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_799
ATGAACAGTCAGCTCAACGGCTTCCACGAGGCGTTCATTGAGGAGGGCACATTCCTCTTCACCTCAGAGTCTGTGGGGGA
AGGCCACCCAGATAAGATTTGTGACCAGATCAGTGATGCTGTGCTTGATGCCCACCTTCAGCAGGACCCTGATGCCAAAG
TAGCTTGTGAACTGTTGGCTAAACTGGGAATGATCCTTCTTGCTGGGGAAATTACATCCAGAGCTGCTGTTGCACTATCC
AGAAAGTGGTTCGTGAAACCATTAAACACATTGGCTATGATGATTCTTCCAAAGGTTTTGACTACAAGACCTGTAATGTG
CTGGTGGCCTTGGAACAACAATCACCAGATATTGCTCAAGGCATTCATCTTGATCGGAATGAGGAAGACATTGGTGCAGG
AGACCAGGGTTTGATGTTTGGTTAAGCCACTGATGAAACTGAAGAGTGTATGCCTTTAACCATTGTCTTAGCACACAAGC
TCAATGCCAAACTGGCTGAACTACGCCGCAATGGCACTTTGCCTTGGCTACGCCCAGATTCTAAAACTCAAGTGACAGTG
CAGTACATGCAGGATTGAGGTGCTGTGCTTCCCATCAGAGTCCACACAATTCTGATATCGGTTCAGCATGATGAAGATGT
TTGTCTTGATGAGATGAGGGATGCCCTAAAGGAGAAAGTCATCAAAGCTGTTGTACCTGCAAAATGCCTTGATGAGGATA
CAATCTACCACCTTCAGCCAAGTGGCAGATTTGTTATTGGTGGGCCTCAGAGTGATGCTGGTTTGACTGGCCGGAAGATC
ATTGTGGACACTTATGGTGGTTGGGGAACTCACGGAGGAGGTGCCTTTTCAGGAAAGGATTATACCAAGGTGGACCGTTC
TGCTGCTTATGCTGCTCGTTGGGTGGCAAAATCCCTTGTTAAAGGAGGTTTATGCAGAAGGTTCTTGTTCAGGTCTCTTA
TGCTATTGGAGTTTCTCATCCATTGTCTATCTCCATTTTCCATTATGGCACCTCTCAGAAGAGTGAGAGAGAGCTATTAG
AGATTGTGAAGAAGAATTTTGACCTCCGCCCTGGGGTCATTGTCAGG
ORF - retro_dnov_799 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.05 % |
| Parental protein coverage: | 91.9 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MNGPVDGLCDHSLSEEGAFMFTSESVGEGHPDKICDQISDAVLDAHLRQDPNAKVACETVCKTGMVLLC- |
| MN....G.......EEG.F.FTSESVGEGHPDKICDQISDAVLDAHL.QDP.AKVACE...K.GM.LL.. | |
| Retrocopy | MNSQLNGFHE-AFIEEGTFLFTSESVGEGHPDKICDQISDAVLDAHLQQDPDAKVACELLAKLGMILLA> |
| Parental | GEITSGAMVDY-QRVVRDTIQHIGYDDSAKGFDFKTCNVLVALEQQSSDIAQCVHLDRNEEDFGAGDQGL |
| G.........Y.Q.VVR.TI.HIGYDDS.KGFD.KTCNVLVALEQQS.DIAQ..HLDRNEED.GAGDQGL | |
| Retrocopy | GKLHPELLLHY>QKVVRETIKHIGYDDSSKGFDYKTCNVLVALEQQSPDIAQGIHLDRNEEDIGAGDQGL |
| Parental | MFGYATDETEECMPLTIILAHKLNARMADLRRSGVLPWLRPDSKTQVTVQYMQDNGAVIPLRIHTIVISV |
| MFG.ATDETEECMPLTI.LAHKLNA..A.LRR.G.LPWLRPDSKTQVTVQYMQD.GAV.P.R.HTI.ISV | |
| Retrocopy | MFG*ATDETEECMPLTIVLAHKLNAKLAELRRNGTLPWLRPDSKTQVTVQYMQD*GAVLPIRVHTILISV |
| Parental | QHDEDIDLEGMRTALKEQVIRAVVPAKYLDEDTIYHLQPSGRFVIGGPQGDAGVTGRKIIVDTYGGWGAH |
| QHDED..L..MR.ALKE.VI.AVVPAK.LDEDTIYHLQPSGRFVIGGPQ.DAG.TGRKIIVDTYGGWG.H | |
| Retrocopy | QHDEDVCLDEMRDALKEKVIKAVVPAKCLDEDTIYHLQPSGRFVIGGPQSDAGLTGRKIIVDTYGGWGTH |
| Parental | GGGAFSGKDYTKVDRSAAYAARWVAKSLVKAGLCRR-VLVQVSYAIGVAEPLSISIFTYGTSRKTERELL |
| GGGAFSGKDYTKVDRSAAYAARWVAKSLVK.GLCRR.VLVQVSYAIGV..PLSISIF.YGTS.K.ERELL | |
| Retrocopy | GGGAFSGKDYTKVDRSAAYAARWVAKSLVKGGLCRR<VLVQVSYAIGVSHPLSISIFHYGTSQKSERELL |
| Parental | DIVNKNFDLRPGVIVR |
| .IV.KNFDLRPGVIVR | |
| Retrocopy | EIVKKNFDLRPGVIVR |
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 | 35 .00 RPM | 0 .58 RPM |
| SRP012922_cerebellum | 33 .68 RPM | 0 .41 RPM |
| SRP012922_heart | 6 .26 RPM | 0 .23 RPM |
| SRP012922_kidney | 15 .06 RPM | 14 .78 RPM |
| SRP012922_liver | 3 .10 RPM | 1175 .60 RPM |
| SRP012922_lung | 25 .66 RPM | 0 .92 RPM |
| SRP012922_quadricep_muscle | 6 .40 RPM | 0 .35 RPM |
| SRP012922_spleen | 32 .05 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_799 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 |