RetrogeneDB ID: retro_dnov_738

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_103271:1719..3051(-)
• 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_738
AGTGCTGAGGAGGAGACCCACCTCAAGAACTATCGGTTCCTGAGAACCATAGGAAAGGGGACCTTTTCTATGATAAAATT
AGCATGACACATCCTCACTGGCCATGAGGTGGCTGTGAAAACCATACAGAAAGATGAAGACACCAGCAGGCTCCTCATGC
TCTCCAGAGAGGTGAGCACAATGAAGACGTTGAGCCATCCCAACATCATCCAGCTGTTTGAAATTATTGAGAACAACAAG
GAACTCTACCTCATCATGGAGTATGCCAGTGGAGGTGATCTCTTTAACTACCTGGTGGCCCAAGGCCCTCTATTAGAACA
GGAAGCCCAAGGGAAATTTCACCAAGTCATGTCTGCCATCCAGTACTGTCACCAGAAATTTATTTCCCACAGGGACTTGA
AAGCAGACAACTTGCTTTTGGATGCTGCTGGGAATGTCAAAGTTGCTGATTTTGGCTTGAGTAATATATTTAACATCGAC
CAGAAGCTGACAACCCTGTGCGGCACTCCCTATTATACTGCCCCTGAAATATTTAAGGAGCACACATACGATGGGCTGCT
GTCGATGTCTAGAGGCTGGGGGTGATTCTGTACACCATGGCCAGTGGGGATCTCCCATTTGCTGCCAGAGCTTCCAGGCC
CTGTGGGAGCAGGTGCTCAGCAGGGAGCTCCCCATTCCAGACCACCTGTCTGTGGATTGTAGGAATCTCCTCAGAAAGTG
CCTGACAGTGGGTCCCTGTAAGAGGACAAGCCACCAGAATGTGATGAGCAACCCGTGAGTAAATACAGGCTGTGAGCACA
AAGAATTGAAGCCATATGTGGAGCTCATATGCCAGGACCCCCACCAGACAGCAATGATAGTTATTATGGGCTACAAAATG
GAAGAGATACAGGAGTCCTTGAGAGATGTGAAACATGACGAGATCATGGCCCATCTATCTCTTGCTGGGCCATAGCAGAT
GGGAGCAGGAGACCTCCACCAGCACCCCACAGACCCAGCCCTCACCTGGCCAGATGCACAGCCACCTTCTTCCTCACACC
ATGTGGAGCAGCACATCGTGTCTGCCCAGCCCAGGCAGCAAAGAGGCAGTGAACCTGTGTTCTCCCCCCTGATTGCTTGT
CTACAGCCCTTCAATACAGGGAGAAGGACCAGAATTCAGGGAGGGAGGCTTGGAGCCTGAGCAACACATATGCCAGCCCC
CTGCCAGGCCAGGAGTGGGAGAAGCCCACCTTTGTGCCCTCCCACCAGAGCTTCCCCCCCTGCCCCAGTCAGCCCTGCAT
CTCTCCTCTCCTGTGGAGGACCAGCCTCAGCCAGGCCTCCATGGACGAGGGC

Alignment

ORF - retro_dnov_738 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.04 %
• Parental protein coverage: 59.95 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SADEQPHIGNYRLLKTIGKGNFAKVKLARHILTGKEVAVKIIDKTQLNSSSLQKLFREVRIMKVLNHPNI
          SA.E..H..NYR.L.TIGKG.F...KLA.HILTG.EVAVK.I.K.....S.L..L.REV..MK.L.HPNI
Retrocopy SAEEETHLKNYRFLRTIGKGTFSMIKLA*HILTGHEVAVKTIQKDE-DTSRLLMLSREVSTMKTLSHPNI

Parental  VKLFEVIETEKTLYLVMEYASGGEVFDYLVAHGRMKEKEARAKFRQIVSAVQYCHQKFIVHRDLKAENLL
          ..LFE.IE..K.LYL.MEYASGG..F.YLVA.G...E.EA..KF.Q..SA.QYCHQKFI.HRDLKA.NLL
Retrocopy IQLFEIIENNKELYLIMEYASGGDLFNYLVAQGPLLEQEAQGKFHQVMSAIQYCHQKFISHRDLKADNLL

Parental  LDADMNIKIADFGFSNEFTFGNKLDTFCGSPPYAAPELFQGKKYDG-PEVDVWSLGVILYTLVSGSLPFD
          LDA..N.K.ADFG.SN.F....KL.T.CG.P.Y.APE.F....YDG...VDV..LGVILYT..SG.LPF.
Retrocopy LDAAGNVKVADFGLSNIFNIDQKLTTLCGTPYYTAPEIFKEHTYDG<AAVDV*RLGVILYTMASGDLPFA

Parental  G-QNLKDLWRQELNEEY-IPVYLSVDCVNLILKFLSIDPCKRTILQHIMHNPWVNVDYEHQELKPNVEPL
          ..Q....LW.Q.L..E..IP..LSVDC.NL..K.L...PCKRT..Q..M.NP.VN...EH.ELKP.VE..
Retrocopy A<QSFQALWEQVLSRELPIPDHLSVDCRNLLRKCLTVGPCKRTSHQNVMSNP*VNTGCEHKELKPYVELI

Parental  VDYQDSHWIAMMVTMGYTMEEVKESLANVKHDLIMA-TYLVLGYSRWEQETSTIVLQPQPSPGQRHCH-P
          ...QD.H..AM.V.MGY.MEE..ESL..VKHD.IMA..YL.LG.SRWEQETST...Q.QPSPGQ.H.H.P
Retrocopy C--QDPHQTAMIVIMGYKMEEIQESLRDVKHDEIMA>IYLLLGHSRWEQETSTSTPQTQPSPGQMHSH<P

Parental  PSPHPVEQHSMSSQPR-QRYSE-SAVLPSDSLFKTI--TEKD-NSGRKA-SMTNTYARPLPDKEWEKPIS
          .S.H.VEQH..S.QPR.QR.SE...VLP.D.L.......EKD.NSGR.A.S..NTYA.PLP..EWEKP..
Retrocopy SSSHHVEQHIVSAQPRQQRGSE<TCVLPPDCLSTALQYREKDQNSGREAWSLSNTYASPLPGQEWEKPTF

Parental  VPSH-SF-PTTSQPCSTPLLQRISLSKAFTDKG
          VPSH.SF.P..SQPC..PLL.R.SLS.A..D.G
Retrocopy VPSHQSFPPCPSQPCISPLLWRTSLSQASMDEG

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_738 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,