RetrogeneDB ID: retro_dnov_1947

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_38320:5894..6141(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000007449
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SRP9
• Ensembl ID: ENSDNOG00000013412
• Aliases: None
• Description: signal recognition particle 9kDa [Source:HGNC Symbol;Acc:11304]

Sequence

>retro_dnov_1947
TACAGTACCAAATCCGTAGTACAGCTTACAGCCGAGAAACTCTACCTCGTGGACCCAATGAAGGCGCGTGTGGTTCTCAA
ATACAGGCATTCTGATGGGAGTCTGTGTATTAAAGTAACAAATGATTTAGTTTGTTTGGTATATAGAAGAGACCAAACAC
AAGGTGTAAAGATCAAGAAATTCCACAATCAACTAATGCAACTTACGGTAGCCAAGGAATGCCGGCAGTGTTGCCATGGA
AATGGAC

Alignment

ORF - retro_dnov_1947 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 96.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YQTWEEFSRAAEKLYLADPMKARVVLKYRHSDGSLCIKVTDDLVCLVYRTDQAQDVKKIEKFHSQLMRLM
          Y.T.......AEKLYL.DPMKARVVLKYRHSDGSLCIKVT.DLVCLVYR.DQ.Q.V.KI.KFH.QLM.L.
Retrocopy YSTKSVVQLTAEKLYLVDPMKARVVLKYRHSDGSLCIKVTNDLVCLVYRRDQTQGV-KIKKFHNQLMQLT

Parental  VAKESR-SVAMETD
          VAKE.R.SVAME.D
Retrocopy VAKECR>SVAMEMD

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	0.39 RPM	35.78 RPM
SRP012922_cerebellum	3.30 RPM	44.26 RPM
SRP012922_heart	0.00 RPM	27.84 RPM
SRP012922_kidney	0.82 RPM	24.09 RPM
SRP012922_liver	0.46 RPM	42.88 RPM
SRP012922_lung	0.76 RPM	43.68 RPM
SRP012922_quadricep_muscle	0.00 RPM	40.50 RPM
SRP012922_spleen	0.92 RPM	29.53 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_1947 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016162	2 retrocopies	retro_cfam_1034, retro_cfam_1527,
Dasypus novemcinctus	ENSDNOG00000013412	3 retrocopies	retro_dnov_1947 , retro_dnov_2181, retro_dnov_742,
Echinops telfairi	ENSETEG00000012291	1 retrocopy	retro_etel_272,
Loxodonta africana	ENSLAFG00000004081	3 retrocopies	retro_lafr_1184, retro_lafr_377, retro_lafr_648,
Otolemur garnettii	ENSOGAG00000001752	1 retrocopy	retro_ogar_230,