RetrogeneDB ID: retro_dnov_676

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_7531:129377..129792(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMAGP
• Ensembl ID: ENSDNOG00000024893
• Aliases: None
• Description: small cell adhesion glycoprotein [Source:HGNC Symbol;Acc:26918]

Sequence

>retro_dnov_676
CCAAGAATCTCTGCCCCTGTTGAGTTCAAAAGGAAGCACCGTGTGGCGCTAGGCCCTCCTCTGGCAGCCTGTTGGACTGG
AAAGGTCTGCTCCTTCCTCAAGGTGTTTGTCCATTGTCCACAGTGACAAGCCTCCCAAGCACACCTTCCCCAAGAGAGGA
AGAACTGATGACCACACCAATTCTGCAGGCCACTGAGTCCTTGTCCCCAGAAGCTGAAGCCAGCACAGCACTATTGCAGT
TGTTATCACCATGGTCTTCCTCATACTGTTCTCGGTCGTGATCTTTATCATCTTTTACGTGGACAAGGACAAAGGTAGCT
GTGTCACTTATAAACCTGAAGAAGGTGAGCTCAGCACCATCCTCCAGAGGGAGAGTGACTCGGCCAAGGGCAGGGAGAGG
GAAGAACATTTCATC

Alignment

ORF - retro_dnov_676 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.79 %
• Parental protein coverage: 84.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PRIPPPS-GAKGSRGRRRAPLRSPS-DWKGRLLPQGTGPLAAMTGHPSTPPPREE-LMTTPILQATESHS
          PRI..P....KGS...R.A.L..P..DWKG.LLPQG..PL...T..PSTP.PREE.LMTTPILQATES.S
Retrocopy PRISAPV>SSKGSTVWR*ALLWQPV>DWKGLLLPQGVCPLSTVTSLPSTPSPREEELMTTPILQATESLS

Parental  PEAEASTAL-IAVVITVVFLTLLSVVILIFFYLYKNKGSYVTYEPAEGEPSATLQMESDSAKGREKEEYF
          PEAEASTAL.IAVVIT.VFL.L.SVVI.I.FY..K.KGS.VTY.P.EGE.S..LQ.ESDSAKGRE.EE.F
Retrocopy PEAEASTAL<IAVVITMVFLILFSVVIFIIFYVDKDKGSCVTYKPEEGELSTILQRESDSAKGREREEHF

Parental  I
          I
Retrocopy I

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	0.19 RPM	15.95 RPM
SRP012922_cerebellum	0.00 RPM	2.89 RPM
SRP012922_heart	0.00 RPM	3.48 RPM
SRP012922_kidney	0.00 RPM	26.56 RPM
SRP012922_liver	0.00 RPM	15.02 RPM
SRP012922_lung	0.00 RPM	25.66 RPM
SRP012922_quadricep_muscle	0.00 RPM	6.75 RPM
SRP012922_spleen	0.00 RPM	9.61 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_676 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001983	1 retrocopy	retro_btau_1742,
Callithrix jacchus	ENSCJAG00000017680	1 retrocopy	retro_cjac_3252,
Dasypus novemcinctus	ENSDNOG00000024893	1 retrocopy	retro_dnov_676 ,
Mus musculus	ENSMUSG00000053559	2 retrocopies	retro_mmus_2330, retro_mmus_3329,