RetrogeneDB ID: retro_dnov_2449

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_75831:2058..2577(-)
• 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_2449
ATGGCCATCACTCAGTTCCGGTTATTTAAAGTTTGTACCTGCCTAGCAACAGTATTCTCATTCCTAAAGAGATTAATATG
CAGATCTGGCAGAGGACGGAAATTAAGTGGAGACCAAATAATTTTGCCAACGACAGTTGATTATTCATCGGTTCCTAAGC
AGACAGATGTTGAAGAGTGGACTTCCTGGGATGAAGATGCACCCACAAGTGTAAAGATTGAAGGAGGGAATGGGAATGTG
GCAGTACAACAAAATGCTTTGGAACAGTTGGAACCCGACTATTTTAAGGACATGACACCAACTATAAGAAAGACTCAAAA
AATTGTTATTAAGAAGAGAGAACCATTAAATTTTGGCATTCCAGATGGAAGCACAGGTTTCTCTAGTAGATTAGCAGCTA
CACAAGATATGCCTTTTATTCATCAATCTCCTGAATTAGGTGACTTAGATACCTGGCAAGAAAATACCAATGCATGGGAG
GAAGAAGAAGATGCAGCCTGGCAAGCAGAAGAAGTTCTG

Alignment

ORF - retro_dnov_2449 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.91 %
• Parental protein coverage: 81.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAITQFRLFKVCTCLATVFSFLKRLICRSGRGRKLSGDQIILTKTVDYSSVPKQTDGQEWTSWDEDAPIS
          MAITQFRLFKVCTCLATVFSFLKRLICRSGRGRKLSGDQIIL..TVDYSSVPKQTD..EWTSWDEDAP.S
Retrocopy MAITQFRLFKVCTCLATVFSFLKRLICRSGRGRKLSGDQIILPTTVDYSSVPKQTDVEEWTSWDEDAPTS

Parental  VKIEGGNGNVAIPPNFWEQLETDYFKDMTPTIRKTPKIVIKKREPLNFGIPDGSTGFSSRLAARQDMPFI
          VKIEGGNGNVA...N..EQLE.DYFKDMTPTIRKT.KIVIKKREPLNFGIPDGSTGFSSRLAA.QDMPFI
Retrocopy VKIEGGNGNVAVQQNALEQLEPDYFKDMTPTIRKTQKIVIKKREPLNFGIPDGSTGFSSRLAATQDMPFI

Parental  HQAPELGDLDTWQENTNAWEEEEDAAWQAEEVL
          HQ.PELGDLDTWQENTNAWEEEEDAAWQAEEVL
Retrocopy HQSPELGDLDTWQENTNAWEEEEDAAWQAEEVL

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	35.39 RPM	1.56 RPM
SRP012922_cerebellum	15.26 RPM	0.96 RPM
SRP012922_heart	7.43 RPM	0.46 RPM
SRP012922_kidney	18.89 RPM	0.55 RPM
SRP012922_liver	10.53 RPM	0.93 RPM
SRP012922_lung	18.94 RPM	1.22 RPM
SRP012922_quadricep_muscle	11.94 RPM	0.35 RPM
SRP012922_spleen	21.75 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_2449 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 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,