RetrogeneDB ID: | retro_dnov_2353 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_66953:1849..3107(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MARK2 | ||
| Ensembl ID: | ENSDNOG00000002037 | ||
| Aliases: | None | ||
| Description: | MAP/microtubule affinity-regulating kinase 2 [Source:HGNC Symbol;Acc:3332] |
Retrocopy-Parental alignment summary:
>retro_dnov_2353
GCAGCCAAGAGTGCTGAGGAGGAGACCCACCTCAAGAACTATCAGTTCCTGAGAACTATAGGAAAGGGGGCCTTTTCTAT
GCTAAAATTAACATGACACATCCTCACCAGTCATGAGGTGGCTGTGAAAATCATACAGAAAGATGAAGACCCCAGCAGGC
TCCTCATGCTCTCCAGAGAGGTCAGCAAAATGAAGACGTTGAGCCATCCCAACATCATCCAGCTGTTTGAAATTATTGAG
AACAACAAGGAACTCTACCTCATCATGGAGTATGCCAGTGGAGGTGATCTCTTTAACTACCTGGTAGCCCAGGGCCCTCT
ATTAGAACAGGAAGCCCAAGGGAAATTTTACCAAGTCATATCTGCCATCCAGTATTGTCACCAGAAATTTATTTCCCACA
GGGACTTGAAAGCAGACAACTTGCTTTTGGATGCTGCTGGGAATGTCAGAGTTGCTGATTTTGGCTTGAGTAATATATTT
AACATCAACCAGTAGCTGACAACCCTGTGCGGCACTCCCTATTATACTGCCCCTGAAGTATTTAAGGAGCACACATATGA
TGGGCCTGCTGTCGATGTCTAGAGGCTGGGGGTAATTCTATACACCATGGCCAGCGGGGATCTCCCATTTGCTGCCAGAG
CTTCCAGGCCCTGTGGGAGCAGGTGCTCAGCGGGGAGCTCCCCATTCCAGGCCACCTGGCTGTGGATTGTAGGAATCTCC
TCAGAAAGTGCCTGACGGTGGATCCCTGTAAGAGGACAGGCTGCCAGAATGTGATGAGCAACCCATGAGTAAGTACGGAC
TGTGAGCACAAAGAATTGAAGCCATATGTGGAGCCCCTCCCAGATTGCCAGGACCCCCACCAGACAGCAATGATAGATAC
TATGGGCTACAAAGTGGAAGAGATACGGGAGTCATTGAGAGCTGTGAAACATGAGATCATGGCCATCTATCTCTTGCTGG
GCCACAGCACATGGGAGCAGGAGACCTCCACCGGTGCCCAACAGACCCAGCTCTCACATGGCCAGAGGCACAGCTGCCCT
CCTTCCCCATACCACGTGAAGCAGCACAGCGTGTCTGCCCAGCCCAGGCAGCAAAGAGGCAGCGAACCTGCGTTCTCCCC
CCTGATTGCTTGTCTACAGCCCTTCAATACAGGGAGAAGGACCAGAATTCAGGGAGGGAGGCTTGGAGCCTGAGGAACGC
ATATGCCAGCCCCCTGCCAGGCCAGGAGTGGGAGAAGCCCACCTCTGTGCCCTTCCAC
ORF - retro_dnov_2353 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 59.43 % |
| Parental protein coverage: | 57.38 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | SATSADEQPHIGNYRLLKTIGKGNFAKVKLARHILTGKEVAVKIIDKTQLNSSSLQKLFREVRIMKVLNH |
| .A.SA.E..H..NY..L.TIGKG.F...KL..HILT..EVAVKII.K.....S.L..L.REV..MK.L.H | |
| Retrocopy | AAKSAEEETHLKNYQFLRTIGKGAFSMLKLT*HILTSHEVAVKIIQKDE-DPSRLLMLSREVSKMKTLSH |
| Parental | PNIVKLFEVIETEKTLYLVMEYASGGEVFDYLVAHGRMKEKEARAKFRQIVSAVQYCHQKFIVHRDLKAE |
| PNI..LFE.IE..K.LYL.MEYASGG..F.YLVA.G...E.EA..KF.Q..SA.QYCHQKFI.HRDLKA. | |
| Retrocopy | PNIIQLFEIIENNKELYLIMEYASGGDLFNYLVAQGPLLEQEAQGKFYQVISAIQYCHQKFISHRDLKAD |
| Parental | NLLLDADMNIKIADFGFSNEFTFGNKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLP |
| NLLLDA..N...ADFG.SN.F.....L.T.CG.P.Y.APE.F....YDGP.VDV..LGVILYT..SG.LP | |
| Retrocopy | NLLLDAAGNVRVADFGLSNIFNINQ*LTTLCGTPYYTAPEVFKEHTYDGPAVDV*RLGVILYTMASGDLP |
| Parental | FDG-QNLKDLWRQELNEEY-IPVYLSVDCVNLILKFLSIDPCKRTILQHIMHNPWVNVDYEHQELKPNVE |
| F...Q....LW.Q.L..E..IP..L.VDC.NL..K.L..DPCKRT..Q..M.NP.V..D.EH.ELKP.VE | |
| Retrocopy | FAA<QSFQALWEQVLSGELPIPGHLAVDCRNLLRKCLTVDPCKRTGCQNVMSNP*VSTDCEHKELKPYVE |
| Parental | PLVDYQDSHWIAMMVTMGYTMEEVKESLANVKHDLIMATYLVLGYSRWEQETSTIVLQPQPSPGQRHCHP |
| PL.D.QD.H..AM..TMGY..EE..ESL..VKH..IMA.YL.LG.S.WEQETST...Q.Q.S.GQRH..P | |
| Retrocopy | PLPDCQDPHQTAMIDTMGYKVEEIRESLRAVKHE-IMAIYLLLGHSTWEQETSTGAQQTQLSHGQRHSCP |
| Parental | PSPHPVEQHSMSSQPR-QRYSESA-VLPSDSLFKTI--TEKD-NSGRKA-SMTNTYARPLPDKEWEKPIS |
| PSP..V.QHS.S.QPR.QR.SE.A.VLP.D.L.......EKD.NSGR.A.S..N.YA.PLP..EWEKP.S | |
| Retrocopy | PSPYHVKQHSVSAQPRQQRGSEPA<VLPPDCLSTALQYREKDQNSGREAWSLRNAYASPLPGQEWEKPTS |
| Parental | VPSH |
| VP.H | |
| Retrocopy | VPFH |
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 .00 RPM | 51 .53 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 24 .33 RPM |
| SRP012922_heart | 0 .00 RPM | 8 .35 RPM |
| SRP012922_kidney | 0 .00 RPM | 15 .06 RPM |
| SRP012922_liver | 0 .00 RPM | 8 .82 RPM |
| SRP012922_lung | 0 .15 RPM | 23 .98 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 7 .96 RPM |
| SRP012922_spleen | 0 .00 RPM | 24 .95 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_2353 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 3 parental genes, and 12 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000002037 | 8 retrocopies |
retro_dnov_1284, retro_dnov_1619, retro_dnov_1691, retro_dnov_2056, retro_dnov_2323, retro_dnov_2353 , retro_dnov_341, retro_dnov_738,
|
| Dasypus novemcinctus | ENSDNOG00000015734 | 1 retrocopy | |
| Tarsius syrichta | ENSTSYG00000000032 | 3 retrocopies |