RetrogeneDB ID: retro_dnov_1241

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_16828:13145..13736(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPK3
• Ensembl ID: ENSDNOG00000002191
• Aliases: None
• Description: mitogen-activated protein kinase 3 [Source:HGNC Symbol;Acc:6877]

Sequence

>retro_dnov_1241
CTGCTGCTCAACACCACCTGCGATCTCAAGATCTGCGACTTTGGCTTGGCCCGTGTGGCAGACCCGGACCATGATCACAC
AGGGTTCCTGACAGAGTATGTAGCCACACGTTGGTACAGGGCTCCAGAGATCATGTTGAATTCCAGGGGGTATACCAAGT
CCATTGACATTGGGTCGGTAGGCTGTATTCTGGCAGAGATGCTTTCCAACAGGCCCATCTTTCCAGGAAAACATTACCTT
GACCAGCTCAACCACATTCTGGGTATTCTTGGATCCCCATCATAGGAAGACCTGAATTGTATTATAAACTTAAAAGCTAG
AAACTATTTGCTTTCTCTTCCACACAAAAATAAGGTGCCATGGAACAGGCTCTTCCCAAATGCTGATTCCAAAGCTCTGG
ACTTACTGGATAAAATGTTGACGTTCAACCCTCACAAGAGGATTGAAGTAGAACAGGCTCTGGCCCACCCGCATCTGCAG
CAGTATTATGATCCAAGTGATGAGCCTGTTGCTGAAGCACCATTCAAGTTTGACATGGAATTGGATGACTTGCCTAAGGA
AAAACTCAAAGAACTCGTTTTCAAAGTGACT

Alignment

ORF - retro_dnov_1241 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.28 %
• Parental protein coverage: 61.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLINTTCDLKICDFGLARIADPEHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSN
          LL.NTTCDLKICDFGLAR.ADP.HDHTGFLTEYVATRWYRAPEIMLNS.GYTKSIDI.SVGCILAEMLSN
Retrocopy LLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSRGYTKSIDIGSVGCILAEMLSN

Parental  RPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLQSLPSKTKVAWAKLFPKSDPKALELLDRML
          RPIFPGKHYLDQLNHILGILGSPS.EDLNCIINLKARNYL.SLP.K.KV.W..LFP..D.KAL.LLD.ML
Retrocopy RPIFPGKHYLDQLNHILGILGSPS*EDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKML

Parental  TFNPNKRITVEEALAHPYLEQYYDPTDEPVAEEPFTFDMELDDLPKERLKELIFQET
          TFNP.KRI.VE.ALAHP.L.QYYDP.DEPVAE.PF.FDMELDDLPKE.LKEL.F..T
Retrocopy TFNPHKRIEVEQALAHPHLQQYYDPSDEPVAEAPFKFDMELDDLPKEKLKELVFKVT

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	21.39 RPM	169.19 RPM
SRP012922_cerebellum	15.40 RPM	64.34 RPM
SRP012922_heart	5.57 RPM	18.33 RPM
SRP012922_kidney	12.05 RPM	57.77 RPM
SRP012922_liver	7.12 RPM	29.26 RPM
SRP012922_lung	12.68 RPM	159.14 RPM
SRP012922_quadricep_muscle	15.92 RPM	16.44 RPM
SRP012922_spleen	19.12 RPM	80.35 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_1241 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017108	1 retrocopy	retro_cfam_1254,
Dasypus novemcinctus	ENSDNOG00000002191	1 retrocopy	retro_dnov_1241 ,
Loxodonta africana	ENSLAFG00000017904	1 retrocopy	retro_lafr_1022,
Myotis lucifugus	ENSMLUG00000011284	1 retrocopy	retro_mluc_1697,
Pongo abelii	ENSPPYG00000007239	1 retrocopy	retro_pabe_1440,
Rattus norvegicus	ENSRNOG00000019601	1 retrocopy	retro_rnor_831,