RetrogeneDB ID: retro_dnov_2056

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_44787:6292..7498(-)
• 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_2056
AAGGAGACCCACCTGAAGAATTATCAGTTCTTGCGATTACTAGGCAAAGGTGGCTTTTCCATGACTTTTCTAGCGCGGCA
TGTCCTCACCCGCCATGAGGTAGCCGTGAAAATCATACACAAGAAGGACAGCCCCAGCAGCCTCCGCATGCGCTCCAGAG
AGGTGAGCATAATGAAGAGCCTGCACCATCCCAACATCGTCCAGCTCTTTGAAGTCATTGACAGCCCGGAGAAGCTCTAC
CTCGTAATGGAGTACGCCCATGGAGGTGATCTCCTGCACTACCTGATGGCCCATGGCCCTCTCTCGGAAGAGGAGGCCCG
AGCAAAATTTCGCCAAGTCTTATCTGCTGTGCAGTACTGTCACCAGAAGTGTATCTCGCACAGAGACTTAAAAGCAGACA
ACCTCCTCTTGGATGCTGCTGGGAATGTGAAAGTTACTGATTTCGGATTAAGTAACACCTTTGACATCAGCCAGCAGCTG
GAAACCCTGTGCGGCACTCCCTGTTATACTGCCCCCGAAATATTTAAGGGGCACACGTACCTTGGGCCGGCCGTGGACGT
CTGGAGCCTGGGGGTGATTCTCTACAACATGGTCAGCGGGAAGTTCCCTTTCTTTGCACAGAGCTCCAAGCTCCTGCAGG
AGCGGGTGCTCAGCGGGGAGTTCCGCATCCCACACTACCTGTCTGTGGACTGCAGGAATCTCCTCCCAAAAGTGCTGACA
GTGGATCCCTGTAGGAGGTCAAGCCTCCCAGACATAATGACTGACCCGTGGGTCAATACGGGCTATGAGCACGCACAACT
GAGGCCGTATGTGGAGCCCCTCCCAGCTCGCCAGGACCCCCACCGGATAGCAGCGATGGTAGCCATGGGCTACAAAGAGG
AGGAGATACAGGCGTCCTTGCAAGATGACAGACATGATGAAGTCATGGCCATATATCTTTTGCTGGGCCACAGCAGATGG
GAGCAGGAGACCTCCACCAGCGCCCCGCAGACCCAGCCCCCTGCCATGCCAGGAGTGGGAGGAGCCCACCTCTGTGCCCT
CCCACCACAGCCTGCCCCCTGCCCTGGTCCACCCTGCAGCTCTCCTCCCCTGCAGAGGACCATCCTCAGTCAGGCCGTCA
TGGACAAGGGCCGGGAGAGCCAGCGCATGCCAGAGCCAGGAGCCTCCAAGACGTCGGCTTCCCCCACAGGGCCCCTGGCC
CTGCCT

Alignment

ORF - retro_dnov_2056 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.09 %
• Parental protein coverage: 53.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EQPHIGNYRLLKTIGKGNFAKVKLARHILTGKEVAVKIIDKTQLNSSSLQKLFREVRIMKVLNHPNIVKL
          ...H..NY..L...GKG.F....LARH.LT..EVAVKII.K.....SSL....REV.IMK.L.HPNIV.L
Retrocopy KETHLKNYQFLRLLGKGGFSMTFLARHVLTRHEVAVKIIHKKD-SPSSLRMRSREVSIMKSLHHPNIVQL

Parental  FEVIETEKTLYLVMEYASGGEVFDYLVAHGRMKEKEARAKFRQIVSAVQYCHQKFIVHRDLKAENLLLDA
          FEVI.....LYLVMEYA.GG....YL.AHG...E.EARAKFRQ..SAVQYCHQK.I.HRDLKA.NLLLDA
Retrocopy FEVIDSPEKLYLVMEYAHGGDLLHYLMAHGPLSEEEARAKFRQVLSAVQYCHQKCISHRDLKADNLLLDA

Parental  DMNIKIADFGFSNEFTFGNKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDGQNL
          ..N.K..DFG.SN.F.....L.T.CG.P.Y.APE.F.G..Y.GP.VDVWSLGVILY..VSG..PF..Q..
Retrocopy AGNVKVTDFGLSNTFDISQQLETLCGTPCYTAPEIFKGHTYLGPAVDVWSLGVILYNMVSGKFPFFAQSS

Parental  KDLWRQELNEEY-IPVYLSVDCVNLILKFLSIDPCKRTILQHIMHNPWVNVDYEHQELKPNVEPLVDYQD
          K.L....L..E..IP.YLSVDC.NL..K.L..DPC.R..L..IM..PWVN..YEH..L.P.VEPL...QD
Retrocopy KLLQERVLSGEFRIPHYLSVDCRNLLPKVLTVDPCRRSSLPDIMTDPWVNTGYEHAQLRPYVEPLPARQD

Parental  SHWIAMMVTMGYTMEEVKESLANVKHDLIMATYLVLGYSRWEQETSTIVLQPQP--SPGQRHCH----PP
          .H.IA.MV.MGY..EE...SL....HD..MA.YL.LG.SRWEQETST...Q.QP...PG....H....PP
Retrocopy PHRIAAMVAMGYKEEEIQASLQDDRHDEVMAIYLLLGHSRWEQETSTSAPQTQPPAMPGVGGAHLCALPP

Parental  SPHPVEQHSMSSQPRQR-YSESAVLPSDSLFKTITEKDNSGRKASMTNTYARP
          .P.P......SS.P.QR.....AV...........E...S...AS.T...A.P
Retrocopy QPAPCPGPPCSSPPLQRTILSQAVMDKGRESQRMPEPGASKTSASPTGPLALP

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	0.62 RPM	8.82 RPM
SRP012922_lung	0.15 RPM	23.98 RPM
SRP012922_quadricep_muscle	0.00 RPM	7.96 RPM
SRP012922_spleen	0.46 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_2056 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,