RetrogeneDB ID: retro_dnov_1619

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_24814:36244..37518(+)
• 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_1619
GCAGCCATGAGTGCTGAGGAGGAGACCCACCTCAAGAACTATTGGTTCCTGAGAACTATAGGATAGGGGGCCTTTTCTAT
GATAAAATTAGCATGACACATCCTCACTGGCCATGAGGTGGCTGTGAAAACCATACAGAAAGATGAAGACCACAGCAGGC
TCCTCATGCTCTCCAGAGAGGTGAGCACAATGAAGATGTTGAGCTATCCCAAAATCATCCAGCTGTTTGAAATTATTGAG
AACAAGGAATTCTACCTCATGATGGAGTATGCCAGTGGAGGTGATCTCTTTAACTACCTGGTAGCCCAGGGCCCTCTATT
AGAACAGGAAGCCCAAGGGAAATTTCACCAAGTCATATCTGCCATCCAGTACTGTTACCAGAAATTTATTTCCCACAGGG
ACTTGAAAGCAGATAACTTGCTTTTGGATGCTGCTGTGAATGTCAAACTTGCTGATTTTGGCTTGAGTAATATATTTAAC
ATCGACCAGTAGCTGACAACCCTGTGTGGCACTCCCTATTATACTGCCCCTGAAATATTTAAGGAGCACACATATGATGG
GCCTGCTGTCGACATCTAGAGGCTGGGTGTGATTCTGTACACCATGGCCAGCAGGGATCTCCCATTTGCTGCACAAAGCT
TCCAGGCCCTGTGGGAGCAGGTGCTCAGTGGGGAGCTCCCCATTCCAGACCACCTGGCTGTGGATTGTAGGAATCTCCTT
ATAAAGTGCCTTATAGTGGGTCCCTATAAGAGGACAAGACTCCAGGATGTGATGAGTGACCCGTGGGTAAATACAGGCTG
TGAGCACAAAGAATTGAAGCCATATGTGGAGCTCCTCCCAGATTGCCAGGACCCCCACCAGACAGCAATGATAGTTACCA
TGGGCTACAAAATGGAAGAGATACAGGAGTCCTTGAGAGATGTGAAACATGATGAGATCATGGCTGTCTATCTCTTGCTG
GGCCACAGCAGATGGGAGCAGGAGACCTCCACCAGCGCCCCACAGACCAAGCCCTCACCTGGTCAGAGGCACAGCCGCCC
TCCTTCCCCACAACACGTGGAGCAGCACATCATATCTGCCCAGCCCAGGTAGCAAAGAGGCAGCAAACCTATGTTCTCCC
CCCTGATTACTTGTCTACAGCCCTTCAATACAGGGAGAAGGACCATAATTTAGGGAGGGAGGTTTGGAGCCTGAGCAACA
CATGTGCCAGCCCCCTGCCAGGCCAGGAGTGGGAGAAGCCCACCTCTGTGCCCTCCCACCAGAGCTTCCCCTCT

Alignment

ORF - retro_dnov_1619 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.41 %
• Parental protein coverage: 57.93 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SATSADEQPHIGNYRLLKTIGKGNFAKVKLARHILTGKEVAVKIIDKTQLNSSSLQKLFREVRIMKVLNH
          .A.SA.E..H..NY..L.TIG.G.F...KLA.HILTG.EVAVK.I.K.....S.L..L.REV..MK.L..
Retrocopy AAMSAEEETHLKNYWFLRTIG*GAFSMIKLA*HILTGHEVAVKTIQKDE-DHSRLLMLSREVSTMKMLSY

Parental  PNIVKLFEVIETEKTLYLVMEYASGGEVFDYLVAHGRMKEKEARAKFRQIVSAVQYCHQKFIVHRDLKAE
          P.I..LFE.IE..K..YL.MEYASGG..F.YLVA.G...E.EA..KF.Q..SA.QYC.QKFI.HRDLKA.
Retrocopy PKIIQLFEIIEN-KEFYLMMEYASGGDLFNYLVAQGPLLEQEAQGKFHQVISAIQYCYQKFISHRDLKAD

Parental  NLLLDADMNIKIADFGFSNEFTFGNKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLP
          NLLLDA..N.K.ADFG.SN.F.....L.T.CG.P.Y.APE.F....YDGP.VD...LGVILYT..S..LP
Retrocopy NLLLDAAVNVKLADFGLSNIFNIDQ*LTTLCGTPYYTAPEIFKEHTYDGPAVDI*RLGVILYTMASRDLP

Parental  FDGQNLKDLWRQELNEEY-IPVYLSVDCVNLILKFLSIDPCKRTILQHIMHNPWVNVDYEHQELKPNVEP
          F..Q....LW.Q.L..E..IP..L.VDC.NL..K.L...P.KRT.LQ..M..PWVN...EH.ELKP.VE.
Retrocopy FAAQSFQALWEQVLSGELPIPDHLAVDCRNLLIKCLIVGPYKRTRLQDVMSDPWVNTGCEHKELKPYVEL

Parental  LVDYQDSHWIAMMVTMGYTMEEVKESLANVKHDLIMATYLVLGYSRWEQETSTIVLQPQPSPGQRHCHPP
          L.D.QD.H..AM.VTMGY.MEE..ESL..VKHD.IMA.YL.LG.SRWEQETST...Q..PSPGQRH..PP
Retrocopy LPDCQDPHQTAMIVTMGYKMEEIQESLRDVKHDEIMAVYLLLGHSRWEQETSTSAPQTKPSPGQRHSRPP

Parental  SPHPVEQHSMSSQPR-QRYS-ESAVLPSDSLFKTI--TEKD-NSGRKA-SMTNTYARPLPDKEWEKPISV
          SP..VEQH..S.QPR.QR.S....VLP.D.L.......EKD.N.GR...S..NT.A.PLP..EWEKP.SV
Retrocopy SPQHVEQHIISAQPR*QRGS<QTYVLPPDYLSTALQYREKDHNLGREVWSLSNTCASPLPGQEWEKPTSV

Parental  PSH-SFPT
          PSH.SFP.
Retrocopy PSHQSFPS

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_1619 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,