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 symbol: MARK2
• Ensembl ID: ENSDNOG00000002037
• Aliases: None
• Description: MAP/microtubule affinity-regulating kinase 2 [Source:HGNC Symbol;Acc:3332]

Sequence

>retro_dnov_2353
GCAGCCAAGAGTGCTGAGGAGGAGACCCACCTCAAGAACTATCAGTTCCTGAGAACTATAGGAAAGGGGGCCTTTTCTAT
GCTAAAATTAACATGACACATCCTCACCAGTCATGAGGTGGCTGTGAAAATCATACAGAAAGATGAAGACCCCAGCAGGC
TCCTCATGCTCTCCAGAGAGGTCAGCAAAATGAAGACGTTGAGCCATCCCAACATCATCCAGCTGTTTGAAATTATTGAG
AACAACAAGGAACTCTACCTCATCATGGAGTATGCCAGTGGAGGTGATCTCTTTAACTACCTGGTAGCCCAGGGCCCTCT
ATTAGAACAGGAAGCCCAAGGGAAATTTTACCAAGTCATATCTGCCATCCAGTATTGTCACCAGAAATTTATTTCCCACA
GGGACTTGAAAGCAGACAACTTGCTTTTGGATGCTGCTGGGAATGTCAGAGTTGCTGATTTTGGCTTGAGTAATATATTT
AACATCAACCAGTAGCTGACAACCCTGTGCGGCACTCCCTATTATACTGCCCCTGAAGTATTTAAGGAGCACACATATGA
TGGGCCTGCTGTCGATGTCTAGAGGCTGGGGGTAATTCTATACACCATGGCCAGCGGGGATCTCCCATTTGCTGCCAGAG
CTTCCAGGCCCTGTGGGAGCAGGTGCTCAGCGGGGAGCTCCCCATTCCAGGCCACCTGGCTGTGGATTGTAGGAATCTCC
TCAGAAAGTGCCTGACGGTGGATCCCTGTAAGAGGACAGGCTGCCAGAATGTGATGAGCAACCCATGAGTAAGTACGGAC
TGTGAGCACAAAGAATTGAAGCCATATGTGGAGCCCCTCCCAGATTGCCAGGACCCCCACCAGACAGCAATGATAGATAC
TATGGGCTACAAAGTGGAAGAGATACGGGAGTCATTGAGAGCTGTGAAACATGAGATCATGGCCATCTATCTCTTGCTGG
GCCACAGCACATGGGAGCAGGAGACCTCCACCGGTGCCCAACAGACCCAGCTCTCACATGGCCAGAGGCACAGCTGCCCT
CCTTCCCCATACCACGTGAAGCAGCACAGCGTGTCTGCCCAGCCCAGGCAGCAAAGAGGCAGCGAACCTGCGTTCTCCCC
CCTGATTGCTTGTCTACAGCCCTTCAATACAGGGAGAAGGACCAGAATTCAGGGAGGGAGGCTTGGAGCCTGAGGAACGC
ATATGCCAGCCCCCTGCCAGGCCAGGAGTGGGAGAAGCCCACCTCTGTGCCCTTCCAC

Alignment

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

Expression

RNA-Seq

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

ChIP-Seq

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST

Dasypus novemcinctus was not studied using EST data.

TSS

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab

retro_dnov_2353 was not experimentally validated.

Homology

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.

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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	retro_dnov_845,
Tarsius syrichta	ENSTSYG00000000032	3 retrocopies	retro_tsyr_1085, retro_tsyr_1471, retro_tsyr_1882,