RetrogeneDB ID: retro_dnov_2477

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_787:77814..78111(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPIL3
• Ensembl ID: ENSDNOG00000002364
• Aliases: None
• Description: peptidylprolyl isomerase (cyclophilin)-like 3 [Source:HGNC Symbol;Acc:9262]

Sequence

>retro_dnov_2477
GGAAGTGGAGGTAACAGTATCTGGGGCAAGCAGTTTGAGGATGAATACAGTGAATATCTTAAGCACAATGTTAGAGGCGG
TGTATCCATGGCGAATAATGGTCCAAACACCACTGGATGCCAGTTCTTCATCATCTTTGGCAAGCAGCCACAGCTGGACA
TGAAGTACACTGTATTTGGACAGGTAATAAATGGTCTAGAGATGCTAGATGAATTGGAGAAGTTACCAGCAAATGAGAAG
ACTTATCAACCTCTTGATGTACACAACAAGGGCATAACTCTTCATGCAAACCCATTT

Alignment

ORF - retro_dnov_2477 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.0 %
• Parental protein coverage: 78.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GRGGSSIWGKKFEDEYSEYLKHNVRGVVSMANNGPNTNGSQFFITYGKQPHLDMKYTVFGKVIDGLETLD
          G.GG.SIWGK.FEDEYSEYLKHNVRG.VSMANNGPNT.G.QFFI..GKQP.LDMKYTVFG.VI.GLE.LD
Retrocopy GSGGNSIWGKQFEDEYSEYLKHNVRGGVSMANNGPNTTGCQFFIIFGKQPQLDMKYTVFGQVINGLEMLD

Parental  ELEKLPVNEKTYRPLNDVHIKDITIHANPF
          ELEKLP.NEKTY.PL.DVH.K.IT.HANPF
Retrocopy ELEKLPANEKTYQPL-DVHNKGITLHANPF

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	8.75 RPM
SRP012922_cerebellum	0.00 RPM	6.74 RPM
SRP012922_heart	0.00 RPM	0.23 RPM
SRP012922_kidney	0.00 RPM	4.93 RPM
SRP012922_liver	0.00 RPM	1.55 RPM
SRP012922_lung	0.00 RPM	2.90 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.38 RPM
SRP012922_spleen	0.00 RPM	5.04 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_2477 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005917	1 retrocopy	retro_amel_1458,
Bos taurus	ENSBTAG00000005416	1 retrocopy	retro_btau_1585,
Canis familiaris	ENSCAFG00000032245	1 retrocopy	retro_cfam_180,
Dasypus novemcinctus	ENSDNOG00000002364	1 retrocopy	retro_dnov_2477 ,
Dipodomys ordii	ENSDORG00000007389	1 retrocopy	retro_dord_575,
Monodelphis domestica	ENSMODG00000015037	1 retrocopy	retro_mdom_1025,
Tupaia belangeri	ENSTBEG00000000664	1 retrocopy	retro_tbel_4520,