RetrogeneDB ID: retro_dnov_2323

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_64031:2567..3846(+)
• 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_2323
GCAGCCATGAGTGCTGAGGAGGAGACCCACCTCAAGAACTATCGGTTCCTGAGAACTATAGGAAAGGGGGCCTTTTCCAT
GATAAAATTAGCACGACACATCCTCACCAGCCATGAGGTGGCTGTGAAAATCATACAGAAAGATGAAGACTCCAGCAGCT
CCTCATGCTCTCCAGAGAGGTCAGCAAAATGAAGATGTTGAGCCATCCTCAAAATCATCCAGTTCTTTGAAATTATTGAG
AACAAGGAATTCTACCTCATGATGGAGTATGCCAGTGGAGGTGATCTCTTTAACTACCTGGTAGCCCAGGGCCCTCTGTT
AGAACAGGAAGCCCAAGGGAAATTTCACCAAGTTATATCTGCCATCCAGTACTGTTACCGGAAATTTATTTCCCACAGGG
ACTTGAAAGCAGATAACTTGCTTTTGGATGCTGCTGTGAATGTCAAACTTGCTGATTTTGGCTTGAGTAATATATTTACC
ATCGACCAGTAGCTGACAACCCTGTGTGGCACTCCCTATTATACTGCCCCTGAAATATTTAAGGAGCACACATATGATGG
GCCTGCTGTCGATGTCTAGAGGCTGGGGGTAATTCTATACACCATGGCCAGCGGGGATCTCCCATTTGCTGCCAGAGCTT
CCAGGCCCTGTGGGAGCAGGTGCTCAGTCGGGAGCTCCCCATTCCAGACCACCTGGCTGTGGATTGTAGGAATCTCCTCA
GAAAGTGCGTTACAGTGGATCCCTGTAAGAGGACAGGCTGCCAGAATGTGATGAGCAACCCATGAGTAAGTACGGACTGT
GAGCACAAAGAATTGAAGGCATATGTGGAGCCCCTCCCAGATTGCCAGGATCCCCACCAGACAGCAATGATAGTTACCAT
GGGCTACAAAATGGAAGAGATACAGGAGTCCTTGAGAGATGTGAAACATGACGAGATCATGGCCGTCTATCTCTTGCTGG
GCCACAGCAGATGGGAGCAGGAGACCTCCACCAGCGCCCAGCAGAACCAGCCCTCACATGGCCAGAGGCACAGCCGCCCT
CCTTCCCCACACCACATGGAGCAGCACAGCATGTCTGCCCAGCCCAGGCAGCAAAGAGGCAGCGAACCTGCCTTCTCCCC
CCTGATTGCTTGTCTACAGTCCTTCAACACAGGGAGAAGGACCAGAATTCAGGGAGGGAGGCTTGGAGCCTGAGCAACAC
ATATGCCAGCCCCCTGCCAGACCAGGAGTGGGAGAAGCCCACCTCTGTGCTCTCCCACCAGAGATCCCCGCCGTCCCAG

Alignment

ORF - retro_dnov_2323 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.51 %
• Parental protein coverage: 58.34 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SATSADEQPHIGNYRLLKTIGKGNFAKVKLARHILTGKEVAVKIIDKTQLNSSS-LQKLFREVRIMKVLN
          .A.SA.E..H..NYR.L.TIGKG.F...KLARHILT..EVAVKII.K....SSS.L..L.REV..MK.L.
Retrocopy AAMSAEEETHLKNYRFLRTIGKGAFSMIKLARHILTSHEVAVKIIQKDE-DSSS<LLMLSREVSKMKMLS

Parental  HPN-IVKLFEVIETEKTLYLVMEYASGGEVFDYLVAHGRMKEKEARAKFRQIVSAVQYCHQKFIVHRDLK
          HP..I...FE.IE..K..YL.MEYASGG..F.YLVA.G...E.EA..KF.Q..SA.QYC..KFI.HRDLK
Retrocopy HPQ>IIQFFEIIEN-KEFYLMMEYASGGDLFNYLVAQGPLLEQEAQGKFHQVISAIQYCYRKFISHRDLK

Parental  AENLLLDADMNIKIADFGFSNEFTFGNKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGS
          A.NLLLDA..N.K.ADFG.SN.FT....L.T.CG.P.Y.APE.F....YDGP.VDV..LGVILYT..SG.
Retrocopy ADNLLLDAAVNVKLADFGLSNIFTIDQ*LTTLCGTPYYTAPEIFKEHTYDGPAVDV*RLGVILYTMASGD

Parental  LPFDG-QNLKDLWRQELNEEY-IPVYLSVDCVNLILKFLSIDPCKRTILQHIMHNPWVNVDYEHQELKPN
          LPF...Q....LW.Q.L..E..IP..L.VDC.NL..K....DPCKRT..Q..M.NP.V..D.EH.ELK..
Retrocopy LPFAA<QSFQALWEQVLSRELPIPDHLAVDCRNLLRKCVTVDPCKRTGCQNVMSNP*VSTDCEHKELKAY

Parental  VEPLVDYQDSHWIAMMVTMGYTMEEVKESLANVKHDLIMATYLVLGYSRWEQETSTIVLQPQPSPGQRHC
          VEPL.D.QD.H..AM.VTMGY.MEE..ESL..VKHD.IMA.YL.LG.SRWEQETST...Q.QPS.GQRH.
Retrocopy VEPLPDCQDPHQTAMIVTMGYKMEEIQESLRDVKHDEIMAVYLLLGHSRWEQETSTSAQQNQPSHGQRHS

Parental  HPPSPHPVEQHSMSSQPR-QRYSESA-VLPSDSLFKTI--TEKD-NSGRKA-SMTNTYARPLPDKEWEKP
          .PPSPH..EQHSMS.QPR.QR.SE.A..LP.D.L.......EKD.NSGR.A.S..NTYA.PLPD.EWEKP
Retrocopy RPPSPHHMEQHSMSAQPRQQRGSEPA<LLPPDCLSTVLQHREKDQNSGREAWSLSNTYASPLPDQEWEKP

Parental  ISVPSHSFPTTSQ
          .SV.SH.....SQ
Retrocopy TSVLSHQRSPPSQ

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_2323 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,