RetrogeneDB ID: retro_dnov_121

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_1850:104781..105617(+)
• Located in intron of: ENSDNOG00000002017

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: MAPKAP1
• Ensembl ID: ENSDNOG00000009733
• Aliases: None
• Description: mitogen-activated protein kinase associated protein 1 [Source:HGNC Symbol;Acc:18752]

Sequence

>retro_dnov_121
GACTTTGGTATTAGAAGACGCTCAAACACAGCTCAAAAATAGGAATGATTCTGGAAAGAGAGACAAAACCAGATGAAATG
CAAAAATATTCATTGGAAAGAAAGAAATTCTAAGCAATCAGCCCAGGAGTTAAAGTTACTCTTTGAAAAAAGGTTCCTCA
AAGAAAACTCTCCAGGGTCTGGAAAGCAGTCAATATCATCTGTATGCCTGGAGCAGGGCCTTCTGCAGCTGAATAACCCT
TTTAGAGTATCCTAAATTTGATGGCAAGGGTCATGTAGGGACAACAGCAACCAAGAAGATCGACATTTACCTCCCCCTGA
ACTCCAGCCAGGACAGACTGTTGCCCATGACTGTGATGACAATGGCCAATGCCAGAGTGCAGGACCTCATTGGGCTCATC
TGTTGGCAGTACACAAGTGAAGGATGGGAGCCAAAGCTCAATGATAATGTCAGTGCCTACTGCCTGCATATTGCTGAGGA
TGATGGGGAGGTTGACACAGATTTCCCCCCGGTGGATTCCAATGAGCCCATTCATAAATTTGGCTTCAGTACTTTGGCCT
TGATTAAAACGTATTCATCCCATGGTCTGACACCTGAAGAGTCACTCTTTGTTCGAATAAATGCTGCTCATGGATTCTCC
CTTATTCAGGTGGACAACACAAAGGACACCAAGAAGGAAATCTTGCTGAAGGTAGTGAAGTGAAGGAAAGGATCCCAGAA
AATTTTAAGCCCTCAGTACCGCCTGGAGAAGCAGAGTGAGCCCAAGGGTGCCAAAGACCTGGAAAGCACCTTGGAGAGCC
AGAGTGCATGGGGGGTTCTGCCTGATCCACGAGAAC

Alignment

ORF - retro_dnov_121 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.82 %
• Parental protein coverage: 62.56 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DFGIRRRSNTAQRLERLRKERQNQXXXXXXXXXXXXXXXXXQELKSLFEKKSLKEKPPSSGKQSILSVRL
          DFGIRRRSNTAQ..E...KERQNQ.................QELK.LFEK..LKE..P.SGKQSI.SV.L
Retrocopy DFGIRRRSNTAQK*E*FWKERQNQMKCKNIHWKERNSKQSAQELKLLFEKRFLKENSPGSGKQSISSVCL

Parental  EQCPLQLNN-PF-NEYSKFDGKGHVGTTATKKIDVYLPLHSSQDRLLPMTVVTMASARVQDLIGLICWQY
          EQ..LQLNN.PF..EY.KFDGKGHVGTTATKKID.YLPL.SSQDRLLPMTV.TMA.ARVQDLIGLICWQY
Retrocopy EQGLLQLNN<PF<LEYPKFDGKGHVGTTATKKIDIYLPLNSSQDRLLPMTVMTMANARVQDLIGLICWQY

Parental  TSEGREPKLXXXXXXXXXHIAEDDGEVDTDFPPLDSNEPIHKFGFSTLALVEKYSSPGLTSKESLFVRIN
          TSEG.EPKL.........HIAEDDGEVDTDFPP.DSNEPIHKFGFSTLAL...YSS.GLT..ESLFVRIN
Retrocopy TSEGWEPKLNDNVSAYCLHIAEDDGEVDTDFPPVDSNEPIHKFGFSTLALIKTYSSHGLTPEESLFVRIN

Parental  AAHGFSLIQVDNTKVTMKEILLKAVKRRKGSQKISGPQYCLEKQSEPNVAVDLESTLESQSAW-EFCLVR
          AAHGFSLIQVDNTK.T.KEILLK.VK.RKGSQKI..PQY.LEKQSEP..A.DLESTLESQSAW..FCL..
Retrocopy AAHGFSLIQVDNTKDTKKEILLKVVK*RKGSQKILSPQYRLEKQSEPKGAKDLESTLESQSAW>GFCLIH

Parental  EN
          EN
Retrocopy EN

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	0.39 RPM	27.23 RPM
SRP012922_cerebellum	0.27 RPM	11.68 RPM
SRP012922_heart	1.16 RPM	10.67 RPM
SRP012922_kidney	0.27 RPM	17.25 RPM
SRP012922_liver	0.15 RPM	10.84 RPM
SRP012922_lung	0.61 RPM	22.30 RPM
SRP012922_quadricep_muscle	1.04 RPM	20.25 RPM
SRP012922_spleen	0.80 RPM	24.49 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_121 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009733	1 retrocopy	retro_dnov_121 ,
Macropus eugenii	ENSMEUG00000005228	1 retrocopy	retro_meug_444,