RetrogeneDB ID: retro_dnov_341

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_3806:120235..121356(+)
• Located in intron of: ENSDNOG00000004051

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_341
AGTCTCTTGAGGGCTAAGGAGGAGACCCACCTGAAGAATTATCAGTTCTTGCGATTACTAGGCAAAGGTGGCTTTTCCAT
GACTTTTCTAGCGCGGCATGTCCTCACCCGCCATGAGGTAGCCGTGAAAATCATACACAAGAAGGACAGCCCCAGCAGCC
TCCGCATGCGCTCCAGAGAGGTGAGCATACTGAAGAGCCTGCACCATCCCAACATCGTCCAGCTCTTTGAAGTCATTGAC
AGCCCGGAGAAGCTCTACCTCGTAATGGAGTACGCCCATGGAGGTGATCTCCTGCACTACCTGATGGCCCATGGCCCTCT
CTCGGAAGAGGAGGCCCGAGCAAAATTTCGCCAAGTCTTATCTGCTGTGCAGTACTGTCACCAGAAGTGTATCTCGCACA
GAGACTTAAAAGCAGACAACCTCCTCTTGGATGCTGCTGGGAATGTGAAAGTTACGGATTTCGGTTTAAGTAATACCTTT
GACATCAGCCAGCAGCTGGAAACCCTGTGCGGCACTCCCTTTTATACTGCCCCCGAAATACTTAAGAGGCACACATACAA
TGGGCCGGCCGTGGATGTCTGGAGCCTGGGGGTGATTCTGTACACCATGGCCAGCGGGGATCTCCCATTTGCTGCCAGAG
CTTCCAGGCCCTGCAGGAGCAAGTGCTCAGCAGGGAGCTCCCCATTCCAGACCACCTGGCTGTGGATTGTAGGAACCTCC
TCAGAAAGTGCCTGACAGTGGATCCCTGTAAGAGGACAAGCCTCCAGGATGTGATGAGTGACCCGTGGGTAAATACGGGC
TGTGAGCACAAAGAATTGAAGCCGTATGTGGAGCCCCTCCCAGATTGCCAGGACCCCCACCAGACAGCAATGATAGTTAC
CATGGGCTACAAAGAGGAGGAGATACAGTCATCCTTGAGAGATGTGAAACATGATGAGATCATGGCCATCTATCTCTTGC
TGGGCCACAGCAGATGGGAGCAGGAGACCTCCACCAGCGCCCCGCAGATCCAGCCCTCACCTGGCCAGAGACGCAGCCGC
CCTCCTTCCCCACACCACATGGAGGAGCACAGTGTGTCTGCCCAGCCCAGGCAGCGAAGAGGCAGCGAATCTGCCATTCT
C

Alignment

ORF - retro_dnov_341 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.37 %
• Parental protein coverage: 50.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SATSADEQPHIGNYRLLKTIGKGNFAKVKLARHILTGKEVAVKIIDKTQLNSSSLQKLFREVRIMKVLNH
          S...A.E..H..NY..L...GKG.F....LARH.LT..EVAVKII.K.....SSL....REV.I.K.L.H
Retrocopy SLLRAKEETHLKNYQFLRLLGKGGFSMTFLARHVLTRHEVAVKIIHKKD-SPSSLRMRSREVSILKSLHH

Parental  PNIVKLFEVIETEKTLYLVMEYASGGEVFDYLVAHGRMKEKEARAKFRQIVSAVQYCHQKFIVHRDLKAE
          PNIV.LFEVI.....LYLVMEYA.GG....YL.AHG...E.EARAKFRQ..SAVQYCHQK.I.HRDLKA.
Retrocopy PNIVQLFEVIDSPEKLYLVMEYAHGGDLLHYLMAHGPLSEEEARAKFRQVLSAVQYCHQKCISHRDLKAD

Parental  NLLLDADMNIKIADFGFSNEFTFGNKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLP
          NLLLDA..N.K..DFG.SN.F.....L.T.CG.P.Y.APE......Y.GP.VDVWSLGVILYT..SG.LP
Retrocopy NLLLDAAGNVKVTDFGLSNTFDISQQLETLCGTPFYTAPEILKRHTYNGPAVDVWSLGVILYTMASGDLP

Parental  FDG-QNLKDLWRQELNEEY-IPVYLSVDCVNLILKFLSIDPCKRTILQHIMHNPWVNVDYEHQELKPNVE
          F...Q....L..Q.L..E..IP..L.VDC.NL..K.L..DPCKRT.LQ..M..PWVN...EH.ELKP.VE
Retrocopy FAA<QSFQALQEQVLSRELPIPDHLAVDCRNLLRKCLTVDPCKRTSLQDVMSDPWVNTGCEHKELKPYVE

Parental  PLVDYQDSHWIAMMVTMGYTMEEVKESLANVKHDLIMATYLVLGYSRWEQETSTIVLQPQPSPGQRHCHP
          PL.D.QD.H..AM.VTMGY..EE...SL..VKHD.IMA.YL.LG.SRWEQETST...Q.QPSPGQR...P
Retrocopy PLPDCQDPHQTAMIVTMGYKEEEIQSSLRDVKHDEIMAIYLLLGHSRWEQETSTSAPQIQPSPGQRRSRP

Parental  PSPHPVEQHSMSSQPRQRY-SESAVL
          PSPH..E.HS.S.QPRQR..SESA.L
Retrocopy PSPHHMEEHSVSAQPRQRRGSESAIL

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_341 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,