RetrogeneDB ID: retro_dnov_2611

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_9023:70634..71005(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPD3
• Ensembl ID: ENSDNOG00000018004
• Aliases: None
• Description: small nuclear ribonucleoprotein D3 polypeptide 18kDa [Source:HGNC Symbol;Acc:11160]

Sequence

>retro_dnov_2611
ATTGGTGTGCCATTAAAGTCCTGCATGACGCGGAGGGCCACATCATGACATGTGAGACAAACACCGGTGAGGTGTATTGG
GAAAAGCTCATTGAGGCAGAGGACAACATGAACTGCCAGATGTCCAACATCACAGTCACCTACAGTGATTGTCGAGTGGC
CCAACTGGGGCAGTCATACATCCACAGCAGCAAGATCTGCTTTCTGATTTTCCCTGACATGCTGAAAAATGCATCCATGT
TAAAGTGTATGAGAAACAAAAACCAAGACTCAAGGGCTGGCTGGGGAAAAACTGCTATTCTGAAGGCCCAAGTGGCTGCA
AGAGGACAAGGCTGTGAAATGGGACATGTAAACATCTTCCAGAAGGGAAGA

Alignment

ORF - retro_dnov_2611 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.8 %
• Parental protein coverage: 98.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IGVP-IKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQXXXITVTYRDGRVAQLEQVYIRGSKIRFL
          IGVP.IKVLH.AEGHI.TCETNTGEVY..KLIEAEDNMNCQ...ITVTY.D.RVAQL.Q.YI..SKI.FL
Retrocopy IGVP<IKVLHDAEGHIMTCETNTGEVYWEKLIEAEDNMNCQMSNITVTYSDCRVAQLGQSYIHSSKICFL

Parental  ILPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVAARGRGRGMGRGNIFQKRR
          I.PDMLKNA.MLK.M.NKNQ.S.AG.GK.AILKAQVAARG.G..MG..NIFQK.R
Retrocopy IFPDMLKNASMLKCMRNKNQDSRAGWGKTAILKAQVAARGQGCEMGHVNIFQKGR

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	51.34 RPM
SRP012922_cerebellum	0.00 RPM	48.39 RPM
SRP012922_heart	0.00 RPM	39.91 RPM
SRP012922_kidney	0.00 RPM	56.68 RPM
SRP012922_liver	0.00 RPM	34.83 RPM
SRP012922_lung	0.00 RPM	65.67 RPM
SRP012922_quadricep_muscle	0.00 RPM	36.00 RPM
SRP012922_spleen	0.00 RPM	61.35 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_2611 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013864	1 retrocopy	retro_cfam_173,
Cavia porcellus	ENSCPOG00000012304	1 retrocopy	retro_cpor_297,
Dasypus novemcinctus	ENSDNOG00000018004	1 retrocopy	retro_dnov_2611 ,
Dipodomys ordii	ENSDORG00000005801	1 retrocopy	retro_dord_791,
Tursiops truncatus	ENSTTRG00000006022	1 retrocopy	retro_ttru_1240,
Vicugna pacos	ENSVPAG00000000241	2 retrocopies	retro_vpac_338, retro_vpac_348,