RetrogeneDB ID: retro_dnov_1284

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_17595:10646..11986(-)
• 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_1284
GCAGCCACAAATGCTGAGGAGCCCACCTCAAGAACTATCGGTTCCTGAGAACCATAGGAAAGGGGGCCTTTTCTATGATG
AAATTAGCACGGCACACCCTCACCGGCCATTAGGTGGCTGTGAAAACCATACAGAAAGATGAAGACCCCAGCAGGCTCCA
CATGCTCTCCAGAGAGGTGAGCACAGTGAAGACGTCGAGCCATCCCAACATCATCCAGCTGTTTGAAATTATTGAGAACA
ACAAGTAACTCTACCTCATGATGGAGTATGCCAGTGGAGGTGATCTCTTTAACTACCTGGTGGCCCAGGACCCTCTATTA
GCACAGGAAGCCCAAGGGAAATTTCACCAAGTCATGTCTGCCATCAGTACTGTCACCAGAAATTTATTTCCCACAGGGAC
TAGAAAGACAACTTGCTTTCAGATGCTGCTGAGAATGTCAGAGTTGCTGATTTGAGCTTGAGTTATATACTTAACATCGA
CCAGAAGCTGACAGCCCTGTGGGGCACTCCCTATTATACTGCCCCTGAGATATTTAAGGGGCACACATACGATGGGCCTG
CTGTCGACATCTAGAGGCTGGGGGTGATTCTGTACACCATGGCCAGCGGGGATCTCCCATTTGCTGCCAGAGCTTCCAGG
CCCTGCAGGAGCAGGTGCTCAACAGGGAGCTCCCCATTCCAGACCACCTGACTGTGGATTGTAGGAATCTCCTCAGAAAG
TTCCTGACAGTGGGTCCCTGTAAAAGAACAAGCCGCCAGAATGTGGTGAGTGACCTGTGGGTAAATACAGGCTGTGAGCA
CAAAGAATTGAAGCCATATGTGGAGCCCCTCCCAGATTGCCAGGACCCCCACCAGACAGCAATGATAGTTACCATGGGCT
ACAAAATGGAAGAGATACAGGAGTCCTTGAGAGATGTGAAACATGACAAGATCATGGCCGTCTATCTCTTGCTGGGCCAC
AGCAGATGGGAGCAGGAGACCTCCACCAGTGCCCCGCAGACCCAGCCCTCACCTGGCCAGAGACGCAGCCGCCCTCCTTC
CTCACACCACATGGAGCAGCACAGCATGTCTGCCCCCAGGCAGCAAAGAGGCAGTGAACCTGCCATTCTCCCTCCTGATT
GCTTGTCTACAGCCTTTCAGTACAGGGAGAAGGACCAGAATTCAGGGAGGGAGGCTTGGAGCCTGAGCAACACATAAGCC
AGCCCCCTGCCAGGCCAGGAGTGGGAGAAGCCCACCTCTCTACCCTCCTACCAGAGCCTGCCCCCTGCCCCAGTCCACCC
TGCTGCTCTCCTCTCCTGCAGAGGACCAGCCTCAGCCAGGCCTTCATGGACGAGGGCCAG

Alignment

ORF - retro_dnov_1284 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.6 %
• Parental protein coverage: 60.49 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SATSADEQP-HIGNYRLLKTIGKGNFAKVKLARHILTGKEVAVKIIDKTQLNSSSLQKLFREVRIMKVLN
          .AT.A.E.P.H..NYR.L.TIGKG.F...KLARH.LTG..VAVK.I.K.....S.L..L.REV...K...
Retrocopy AATNA-EEP<HLKNYRFLRTIGKGAFSMMKLARHTLTGH*VAVKTIQKDE-DPSRLHMLSREVSTVKTSS

Parental  HPNIVKLFEVIETEKTLYLVMEYASGGEVFDYLVAHGRMKEKEARAKFRQIVSAV-QYCHQKFIVHRDLK
          HPNI..LFE.IE..K.LYL.MEYASGG..F.YLVA.......EA..KF.Q..SA..QYCHQKFI.HRD.K
Retrocopy HPNIIQLFEIIENNK*LYLMMEYASGGDLFNYLVAQDPLLAQEAQGKFHQVMSAI<QYCHQKFISHRD*K

Parental  AENLLLDADMNIKIADFGFSNEFTFGNKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGS
          ..NLL.DA..N...AD...S.......KL....G.P.Y.APE.F.G..YDGP.VD...LGVILYT..SG.
Retrocopy -DNLLSDAAENVRVADLSLSYILNIDQKLTALWGTPYYTAPEIFKGHTYDGPAVDI*RLGVILYTMASGD

Parental  LPFDG-QNLKDLWRQELNEEY-IPVYLSVDCVNLILKFLSIDPCKRTILQHIMHNPWVNVDYEHQELKPN
          LPF...Q....L..Q.LN.E..IP..L.VDC.NL..KFL...PCKRT..Q......WVN...EH.ELKP.
Retrocopy LPFAA<QSFQALQEQVLNRELPIPDHLTVDCRNLLRKFLTVGPCKRTSRQNVVSDLWVNTGCEHKELKPY

Parental  VEPLVDYQDSHWIAMMVTMGYTMEEVKESLANVKHDLIMATYLVLGYSRWEQETSTIVLQPQPSPGQRHC
          VEPL.D.QD.H..AM.VTMGY.MEE..ESL..VKHD.IMA.YL.LG.SRWEQETST...Q.QPSPGQR..
Retrocopy VEPLPDCQDPHQTAMIVTMGYKMEEIQESLRDVKHDKIMAVYLLLGHSRWEQETSTSAPQTQPSPGQRRS

Parental  HPPSPHPVEQHSMSSQPRQRYSESAVLPSDSL---FKTITEKDNSGRKA-SMTNTYARPLPDKEWEKPIS
          .PPS.H..EQHSMS....QR.SE.A.LP.D.L...F.......NSGR.A.S..NT.A.PLP..EWEKP.S
Retrocopy RPPSSHHMEQHSMSAPRQQRGSEPAILPPDCLSTAFQYREKDQNSGREAWSLSNT*ASPLPGQEWEKPTS

Parental  VPSHSF--PTTSQPCS-TPLLQRISLSKAFTDKGE
          .PS.....P....P....PLLQR.SLS.AF.D.G.
Retrocopy LPSYQSLPPAPVHPAA<SPLLQRTSLSQAFMDEGQ

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	0.00 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_1284 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.

---

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,