RetrogeneDB ID: retro_dnov_792

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_107970:3894..4343(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000000496
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SZRD1
• Ensembl ID: ENSDNOG00000011616
• Aliases: None
• Description: SUZ RNA binding domain containing 1 [Source:HGNC Symbol;Acc:30232]

Sequence

>retro_dnov_792
CAAGATGAGGAGGTCACTGAGAGCTGGGAAGAGGCACCAGACAGTGGGCAAATGGACAGTTGGATAAAAACATGAAGATC
ACACAAAAGAAAAGGAGAGCGGGAAACCCAAATCTCCCAAAGTGCCCTTCGTGATTCAGGATGATAGCCTTCCGACCGGT
GCCCTCCACAGATCCACATCCTCAAGAGGTCCACCAGCAATGGTGTGGTCAGCAGCCCCAACTCCACCAGCAGGCCAGCA
CTTCCAGTCAAGTCCTTATCCCAGCAGGAGGCAGAGTTTGCCAAGGCTTGGAAGCAGGTCCTGGGCAGTGCCAACCTTAG
GAGGAGCAGGAGAAACCCATCCTCGACAGACTAACCAGAATCTCCCAGCCTGAAGACAGCAGGCGGCCCAATAATGTGAT
TGCTCAGCCCTTGGGTCCTGATGGGTCACAAGGGTTCAAACAGCACAGA

Alignment

ORF - retro_dnov_792 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.03 %
• Parental protein coverage: 99.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EDEEVAESWEEAADSGEIDRRLEKKLKITQKESR-KSKSPPKVPIVIQDDSLPTGP-PPQIRILKRPTSN
          .DEEV.ESWEEA.DSG..D...........K..R.K.KS.PKVP.VIQDDSLPTG..PPQI.ILKR.TSN
Retrocopy QDEEVTESWEEAPDSGQMDSWIKT*RSHKRKGER>KPKS-PKVPFVIQDDSLPTGA<PPQIHILKRSTSN

Parental  GVVSSPNSTSRPALPVKSLAQREAEYAEARKRILGSAS-PEEEQEKPILDRPTRISQPEDSRQPNNVIRQ
          GVVSSPNSTSRPALPVKSL.Q.EAE.A.A.K..LGSA..P.EEQEKPILDR.TRISQPEDSR.PNNVI.Q
Retrocopy GVVSSPNSTSRPALPVKSLSQQEAEFAKAWKQVLGSAN<P*EEQEKPILDRLTRISQPEDSRRPNNVIAQ

Parental  PLGPDGSQGFKQRR
          PLGPDGSQGFKQ.R
Retrocopy PLGPDGSQGFKQHR

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	37.53 RPM
SRP012922_cerebellum	0.00 RPM	10.45 RPM
SRP012922_heart	0.00 RPM	9.98 RPM
SRP012922_kidney	0.00 RPM	12.87 RPM
SRP012922_liver	0.00 RPM	19.04 RPM
SRP012922_lung	0.00 RPM	21.53 RPM
SRP012922_quadricep_muscle	0.00 RPM	21.29 RPM
SRP012922_spleen	0.00 RPM	26.44 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_792 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008232	2 retrocopies	retro_cjac_1000, retro_cjac_3307,
Dasypus novemcinctus	ENSDNOG00000011616	1 retrocopy	retro_dnov_792 ,