RetrogeneDB ID: retro_dnov_187

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_2432:254839..255363(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: E2F6
• Ensembl ID: ENSDNOG00000000258
• Aliases: None
• Description: E2F transcription factor 6 [Source:HGNC Symbol;Acc:3120]

Sequence

>retro_dnov_187
ATCACCAATGACTTAGACGGAATTGGCCTAGTTAAAAAAAACCTAAGAACTGTATTCAGTGGATAGGAGCTGATCTTAGC
GATTTTGGAGCAATACCCCAGCAAACGTAGCCACAGGAGGAACTTTCTGACTTATCAGCAATGGAAGATGCTTTGGATGA
GTTAATTAAGGATTGTGCTTAGCATGTGTTTGAATTAACAAATGACAAAGAAAATCAAAGACTAGCATATGTGACTTATC
AAGATATTCATAGCATTTGAGCCTTCCATGAACAGATTGTTATTGTAGGTAAAGCTCCAGCAGAAACAAAATCGGATGTT
CCAGCTCCCAGAGAAGACTCTATAACAGTCCATATAAGGAGCACCAAAGCACCTACTGATGTTTGTTTATGTGAAGTGGG
GCAGGATAACACAAGTAACGAAGTATCTGAAGATGTAGGGACCTCTTCATCTGAAAGGAAGCCTCTCAAATACACTGATG
AAGAAGAAAATCCTCTTTAGCAAAGTGAAGAATCACTTGACGTG

Alignment

ORF - retro_dnov_187 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.16 %
• Parental protein coverage: 71.02 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ITNVLDGIDLVEKK-SKNHIRWIGSDLSDFGAIPQQKKLQEELSDLSAMEDALDELIKDCAQQLFELTDD
          ITN.LDGI.LV.....KN.I.WIG.DLSDFGAIPQQ...QEELSDLSAMEDALDELIKDCA...FELT.D
Retrocopy ITNDLDGIGLVXXX<PKNCIQWIGADLSDFGAIPQQT*PQEELSDLSAMEDALDELIKDCA*HVFELTND

Parental  KENERLAYVTYQDIHSIRAFHEQIVIAVKAPAETRLDVPAPREDSITVHIRSTKGPIDVYLCEVEQDSTS
          KEN.RLAYVTYQDIHSI.AFHEQIVI..KAPAET..DVPAPREDSITVHIRSTK.P.DV.LCEV.QD.TS
Retrocopy KENQRLAYVTYQDIHSI*AFHEQIVIVGKAPAETKSDVPAPREDSITVHIRSTKAPTDVCLCEVGQDNTS

Parental  NKVSEEAGAASESKLPAR-PGEESIDHPQSEELLEV
          N.VSE..G..S....P.....EE.....QSEE.L.V
Retrocopy NEVSEDVGTSSSERKPLKYTDEEENPL*QSEESLDV

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	2.92 RPM
SRP012922_cerebellum	0.00 RPM	8.66 RPM
SRP012922_heart	0.00 RPM	3.02 RPM
SRP012922_kidney	0.00 RPM	4.38 RPM
SRP012922_liver	0.00 RPM	1.08 RPM
SRP012922_lung	0.00 RPM	5.50 RPM
SRP012922_quadricep_muscle	0.00 RPM	7.62 RPM
SRP012922_spleen	0.00 RPM	9.16 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_187 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 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000048286	1 retrocopy	retro_btau_1820,
Callithrix jacchus	ENSCJAG00000006910	1 retrocopy	retro_cjac_178,
Dasypus novemcinctus	ENSDNOG00000000258	1 retrocopy	retro_dnov_187 ,
Homo sapiens	ENSG00000169016	4 retrocopies	retro_hsap_2542, retro_hsap_2547, retro_hsap_2572, retro_hsap_4906,
Macropus eugenii	ENSMEUG00000007957	4 retrocopies	retro_meug_1169, retro_meug_860, retro_meug_882, retro_meug_893,
Myotis lucifugus	ENSMLUG00000003384	1 retrocopy	retro_mluc_864,
Macaca mulatta	ENSMMUG00000023225	1 retrocopy	retro_mmul_87,
Nomascus leucogenys	ENSNLEG00000014134	1 retrocopy	retro_nleu_2351,
Pongo abelii	ENSPPYG00000012646	1 retrocopy	retro_pabe_1,
Pan troglodytes	ENSPTRG00000011661	2 retrocopies	retro_ptro_1484, retro_ptro_3272,
Ictidomys tridecemlineatus	ENSSTOG00000003316	1 retrocopy	retro_itri_135,