RetrogeneDB ID: retro_dnov_1279

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_175598:3555..3780(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NPM3
• Ensembl ID: ENSDNOG00000018876
• Aliases: None
• Description: nucleophosmin/nucleoplasmin 3 [Source:HGNC Symbol;Acc:7931]

Sequence

>retro_dnov_1279
CTCTCTGGCTGTACCCACTCCTTCACCTTCAAGATAGAGGAAGAGGATAATGCAGAGCGCATGCTGGCACTGCCCATGCT
CTGTCTCACTGAGGCGGCCATGGATGAGCATCATGTGGTGGATGTTGGGACCCAGAACAATCACCATCAGGAGATCACAG
TCTCCGTGGCCAACCTCACAGTTGTCCTGCCAACCCAAGCTCAGCCCAACCCCCTGTAACCTCCC

Alignment

ORF - retro_dnov_1279 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.0 %
• Parental protein coverage: 55.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSGGTRSYTFEVEEEDDGEHVLALTMLCLTEGAKDECNVVEIVAQNNDHYEMAVPVANLKSCQPMLSPDD
          LSG.T.S.TF..EEED..E..LAL.MLCLTE.A.DE..VV....QNN.H.E..V.VANL....P......
Retrocopy LSGCTHSFTFKIEEEDNAERMLALPMLCLTEAAMDEHHVVDVGTQNNHHQEITVSVANLTVVLPTQAQPN

Parental  QLHSP
          .L..P
Retrocopy PL*PP

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	0.97 RPM
SRP012922_cerebellum	0.14 RPM	7.29 RPM
SRP012922_heart	0.00 RPM	0.23 RPM
SRP012922_kidney	0.00 RPM	1.10 RPM
SRP012922_liver	0.15 RPM	0.15 RPM
SRP012922_lung	0.15 RPM	1.53 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.87 RPM
SRP012922_spleen	0.00 RPM	0.92 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_1279 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 18 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017639	2 retrocopies	retro_amel_1233, retro_amel_90,
Bos taurus	ENSBTAG00000016335	1 retrocopy	retro_btau_1164,
Canis familiaris	ENSCAFG00000009919	2 retrocopies	retro_cfam_1968, retro_cfam_2064,
Callithrix jacchus	ENSCJAG00000017650	2 retrocopies	retro_cjac_2491, retro_cjac_3052,
Cavia porcellus	ENSCPOG00000006301	1 retrocopy	retro_cpor_1315,
Dasypus novemcinctus	ENSDNOG00000018876	1 retrocopy	retro_dnov_1279 ,
Dipodomys ordii	ENSDORG00000003491	1 retrocopy	retro_dord_577,
Felis catus	ENSFCAG00000007178	1 retrocopy	retro_fcat_1906,
Homo sapiens	ENSG00000107833	1 retrocopy	retro_hsap_792,
Macropus eugenii	ENSMEUG00000003465	2 retrocopies	retro_meug_20, retro_meug_25,
Microcebus murinus	ENSMICG00000011739	1 retrocopy	retro_mmur_126,
Myotis lucifugus	ENSMLUG00000004961	1 retrocopy	retro_mluc_2333,
Macaca mulatta	ENSMMUG00000015774	1 retrocopy	retro_mmul_1072,
Mustela putorius furo	ENSMPUG00000016894	2 retrocopies	retro_mputfur_750, retro_mputfur_759,
Mus musculus	ENSMUSG00000056209	2 retrocopies	retro_mmus_2756, retro_mmus_3479,
Ochotona princeps	ENSOPRG00000009229	2 retrocopies	retro_opri_1019, retro_opri_92,
Pongo abelii	ENSPPYG00000002589	1 retrocopy	retro_pabe_706,
Pan troglodytes	ENSPTRG00000002875	1 retrocopy	retro_ptro_551,