RetrogeneDB ID: retro_dnov_257

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_3069:95398..95633(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZCCHC10
• Ensembl ID: ENSDNOG00000017302
• Aliases: None
• Description: zinc finger, CCHC domain containing 10 [Source:HGNC Symbol;Acc:25954]

Sequence

>retro_dnov_257
GAAGCACATAAGCAACATATAAGATATCAGAATGCTTATAATTTGGACATTGGCCTTATGAATGTGTGGGAAAAGAAAAT
ACTTATATAGGCCTTCGAGAATACCAGAACTAAAGAAAGCTTTAAAAGAAAGAGAAAGCAGGTTATTATAACAAAGCATT
GGAGAACCTAATGTAGAAAAAAAGACCAAGAAAAAAAGGTCTAAGCATGTAACCAGTTCAAATAGCAATGGCAGT

Alignment

ORF - retro_dnov_257 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.41 %
• Parental protein coverage: 70.8 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EANKQHVRCQ-KCLEFGHWTYECTGK-RKYLHRPSRTAELKKALKEKENRLLLQQSIGETNVEKKTKKKR
          EA.KQH.R.Q..CL.FGHW.YEC.GK.RKYL.RPSR..ELKKALKE.E.R.LL.QSIGE.NV........
Retrocopy EAHKQHIRYQ<ECL*FGHWPYECVGK<RKYLYRPSRIPELKKALKERESR-LL*QSIGEPNVXXXXXXXX

Parental  SSVSSSSNSSGS
          S....SSNS.GS
Retrocopy SKHVTSSNSNGS

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	2.14 RPM
SRP012922_cerebellum	0.00 RPM	1.79 RPM
SRP012922_heart	0.00 RPM	1.62 RPM
SRP012922_kidney	0.00 RPM	0.82 RPM
SRP012922_liver	0.00 RPM	0.46 RPM
SRP012922_lung	0.15 RPM	1.53 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.21 RPM
SRP012922_spleen	0.00 RPM	2.29 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_257 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 10 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031203	1 retrocopy	retro_cfam_643,
Choloepus hoffmanni	ENSCHOG00000001420	9 retrocopies	retro_chof_1243, retro_chof_1263, retro_chof_1773, retro_chof_2048, retro_chof_2132, retro_chof_2183, retro_chof_501, retro_chof_790, retro_chof_923,
Dasypus novemcinctus	ENSDNOG00000017302	1 retrocopy	retro_dnov_257 ,
Myotis lucifugus	ENSMLUG00000011366	4 retrocopies	retro_mluc_172, retro_mluc_2240, retro_mluc_2241, retro_mluc_2574,
Monodelphis domestica	ENSMODG00000013827	1 retrocopy	retro_mdom_1405,
Mus musculus	ENSMUSG00000018239	1 retrocopy	retro_mmus_269,
Otolemur garnettii	ENSOGAG00000032171	1 retrocopy	retro_ogar_3011,
Pongo abelii	ENSPPYG00000015776	1 retrocopy	retro_pabe_2395,
Rattus norvegicus	ENSRNOG00000006943	3 retrocopies	retro_rnor_2037, retro_rnor_2528, retro_rnor_801,
Sorex araneus	ENSSARG00000007221	1 retrocopy	retro_sara_639,