RetrogeneDB ID: retro_dnov_1014

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_135089:417..921(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EBAG9
• Ensembl ID: ENSDNOG00000007465
• Aliases: None
• Description: estrogen receptor binding site associated, antigen, 9 [Source:HGNC Symbol;Acc:3123]

Sequence

>retro_dnov_1014
ATGGCTATCATACAGTTCCAGTTATTTAAAGTTTGTGCTTCCTAGCAACAGTATTCTCATTCTTAAAGACACTAATATGC
AGATTTGGCAGAGGATGGAAATTAAGGGGAGACCAAATAACTTTGCCAACTACAGTTGATTACTCATTGGTTCTTAAGTA
GACAGATGTTGAAGACTTCCTGGCTTGAAGATGCACCCACAAGTGTATTGATCAAAGGAGGGAATGGGAATGTGGCAACA
CAACAAAATGCTTTGGAACAGCTGGAACCTGACTATTTTAAGGACAAGACACCAACTTTAAGAAAGACTCAGAAAAATGT
TATTAAGAAGAGAGAACCATTAAATTTTGGCATTCCAATTGGAAGCACAGTTTTCTCTAGTAGATTAGCAGCTATGCCTT
TTATTCATCAAACTCCTGAATTAGGTGATTTAGATAACTGGCAAGAAAATACCAATTCATGAAAGGAAGAAGAAGATACA
ACCTGGCAAGCAGAAAAAGTTGTG

Alignment

ORF - retro_dnov_1014 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.29 %
• Parental protein coverage: 81.6 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAITQFRLFKVCTC-LATVFSFLKRLICRSGRGRKLSGDQIILTKTVDYSSVPKQTDGQEWTS-WDEDAP
          MAI.QF.LFKVC...LATVFSFLK.LICR.GRG.KL.GDQI.L..TVDYS.V.K.TD........D....
Retrocopy MAIIQFQLFKVCAS<LATVFSFLKTLICRFGRGWKLRGDQITLPTTVDYSLVLK*TDVEDFLA>EDAPTS

Parental  ISVKIEGGNGNVAIPPNFWEQLETDYFKDMTPTIRKTPKIVIKKREPLNFGIPDGSTGFSSRLAARQDMP
          ...K...GN..VA...N..EQLE.DYFKD.TPT.RKT.K.VIKKREPLNFGIP.GST.FSSRLAA...MP
Retrocopy VLIKGGNGN--VATQQNALEQLEPDYFKDKTPTLRKTQKNVIKKREPLNFGIPIGSTVFSSRLAA---MP

Parental  FIHQAPELGDLDTWQENTNAWEEEEDAAWQAEEVL
          FIHQ.PELGDLD.WQENTN...EEED..WQAE.V.
Retrocopy FIHQTPELGDLDNWQENTNS*KEEEDTTWQAEKVV

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	1.56 RPM
SRP012922_cerebellum	0.00 RPM	0.96 RPM
SRP012922_heart	0.00 RPM	0.46 RPM
SRP012922_kidney	0.00 RPM	0.55 RPM
SRP012922_liver	0.00 RPM	0.93 RPM
SRP012922_lung	0.00 RPM	1.22 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.35 RPM
SRP012922_spleen	0.00 RPM	0.92 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_1014 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 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000007465	2 retrocopies	retro_dnov_1014 , retro_dnov_2449,
Macropus eugenii	ENSMEUG00000014115	3 retrocopies	retro_meug_1871, retro_meug_2058, retro_meug_597,
Monodelphis domestica	ENSMODG00000004795	2 retrocopies	retro_mdom_261, retro_mdom_665,
Pongo abelii	ENSPPYG00000018824	1 retrocopy	retro_pabe_622,
Pan troglodytes	ENSPTRG00000020513	1 retrocopy	retro_ptro_515,