RetrogeneDB ID: retro_dnov_2601

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_89358:4865..5165(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDCA5
• Ensembl ID: ENSDNOG00000019033
• Aliases: None
• Description: cell division cycle associated 5 [Source:HGNC Symbol;Acc:14626]

Sequence

>retro_dnov_2601
AAGCCCATGGTCCTGAAGAAGACAGTGGCCCATGCCTTAGAGGTCCCAGCTCTCCATCGCCTCGCAGGAGCCCTAGCATT
GCCTTTTTCCTGGAGAAAGAAAACAACCCTCCTAGCAAGGAACCTACCAAGGAGGACCTCGACATGCAGCGTGTCTGTCA
CCTCAGCCACCGCTCCCAGGGCTGTACCCCTTGAACCTCGATCTAGCTCCAAAGAAGGACACCCAGATGCCAGAGTCTTG
GAAATGTCTAAGAAAGTCAGGCTGTCCTACACCCGGCTAGAGTCTCTCGGCTCTGCCTCC

Alignment

ORF - retro_dnov_2601 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.65 %
• Parental protein coverage: 54.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KTIGLERIVAHVLEVPAVQ-SPRRSPRIAFFLEKGNNPPRKETTKEDLFQ-TSSVPVTTATTPVLYPLEV
          K...L...VAH.LEVPA...SPRRSP.IAFFLEK.NNPP.KE.TKEDL.....SV...TA..P...PLE.
Retrocopy KPMVLKKTVAHALEVPALH<SPRRSPSIAFFLEKENNPPSKEPTKEDLDM>SVSVTSATA--PRAVPLEP

Parental  KSNSKKGHPDPRDLEMSTKVRRPASTLASTGRRS
          .S.SK.GHPD.R.LEMS.KVR.....L.S.G..S
Retrocopy RSSSKEGHPDARVLEMSKKVRLSYTRLESLGSAS

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	0.19 RPM	0.00 RPM
SRP012922_cerebellum	0.14 RPM	0.00 RPM
SRP012922_heart	0.00 RPM	0.00 RPM
SRP012922_kidney	0.00 RPM	0.00 RPM
SRP012922_liver	0.00 RPM	0.00 RPM
SRP012922_lung	0.00 RPM	0.00 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.00 RPM
SRP012922_spleen	0.00 RPM	0.00 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_2601 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002502	1 retrocopy	retro_cjac_4145,
Dasypus novemcinctus	ENSDNOG00000019033	1 retrocopy	retro_dnov_2601 ,
Felis catus	ENSFCAG00000028197	1 retrocopy	retro_fcat_761,
Pteropus vampyrus	ENSPVAG00000007908	1 retrocopy	retro_pvam_567,
Rattus norvegicus	ENSRNOG00000046635	2 retrocopies	retro_rnor_639, retro_rnor_640,