RetrogeneDB ID: retro_dnov_1621

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_24864:35708..36077(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000000677
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SH3BGRL3
• Ensembl ID: ENSDNOG00000016833
• Aliases: None
• Description: SH3 domain binding glutamic acid-rich protein like 3 [Source:HGNC Symbol;Acc:15568]

Sequence

>retro_dnov_1621
AGGAAACTGTTCCCAAGAACAGCAGTGTCATCTCCCAGTCATGCAGCTGCTATTATGGCTGATCCATCCGTCGGCCAGTC
AGTCCACCAACAGCATGAATGGCTTGTGCATCAACAGCAGGTCAGTCACTGGTTCCCATGAAATCAAGTTCCAGCAGAGT
GAAGTGACAGCATCCTAGACAGGAAGCACATCCAGTGCCAGGTAGTGGATATCTCCCAGGACAATGTCCTGCAGGATGAG
ATGTACACCTTGGTGGGCCTCCAAGGGCACCTCACCCCAGATTGTCAATGGGGATCACGACTCTGAGACTCTGAGGTCTT
TGTGGAGGCTGTGGAACAAAACACACTGCAGGAGTTCCTGAAACTGGCT

Alignment

ORF - retro_dnov_1621 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.94 %
• Parental protein coverage: 56.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RKPLPSAAASSPRCAAAATAALRLTTS-STRSMSGLRVYSTSVTGSREIKSQQSEVTR-ILDGKRIQYEL
          RK..P..A.SSP..AAA..A......S.ST.SM.GL...S.SVTGS.EIK.QQSEVT..ILD.K.IQ...
Retrocopy RKLFPRTAVSSPSHAAAIMADPSVGQS>STNSMNGLCINSRSVTGSHEIKFQQSEVTA<ILDRKHIQCQV

Parental  VDISQDNALRDEMRALAGNPKATPPQIVNGNQYCGDYELFVEAVEQNTLQEFLKLA
          VDISQDN.L.DEM..L.G......P....G.....D.E.FVEAVEQNTLQEFLKLA
Retrocopy VDISQDNVLQDEMYTLVGLQGHLTPDCQWGSRL*-DSEVFVEAVEQNTLQEFLKLA

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	114.74 RPM
SRP012922_cerebellum	0.00 RPM	57.05 RPM
SRP012922_heart	0.00 RPM	10.44 RPM
SRP012922_kidney	0.00 RPM	73.92 RPM
SRP012922_liver	0.00 RPM	26.63 RPM
SRP012922_lung	0.31 RPM	133.02 RPM
SRP012922_quadricep_muscle	0.00 RPM	7.96 RPM
SRP012922_spleen	0.00 RPM	135.41 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_1621 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000016833	1 retrocopy	retro_dnov_1621 ,
Macropus eugenii	ENSMEUG00000007201	1 retrocopy	retro_meug_388,