RetrogeneDB ID: retro_dnov_875

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_1169:226164..226489(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBY1
• Ensembl ID: ENSDNOG00000010982
• Aliases: None
• Description: chibby homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:1307]

Sequence

>retro_dnov_875
AGTCAGCCTCTCTGAAATCTGCATTCTTTGAATCGGTCAACTCAAGAGAATGAGTTAGACCTTGACTTTGGATCTCTACT
ATTATTCAGGCAGGGCAAAGCCTGACATCTGAGAATGGCCAGTGGATCTCAGACACATGGATTGGTGAAGGCACAGATGG
AAGGAGACTTAGCACATTCATGGGCAAAACCAGCGTTTGGAAGAAACAAATAATCAACTGTGACTAAAAGTGGACATTCT
CCTAAACATGCAACCAGGGACCACAGTTGAGTTGCACTTAATGGGGAAGGAATAAGATAAACTAAAGAGCTTCACCAGCA
GGAGA

Alignment

ORF - retro_dnov_875 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.76 %
• Parental protein coverage: 85.83 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SASLSNLHSLDRSTRDVELGLDYGT-PTMNLAGQSLKFENGQWIAETGISGGVDRR-EAQRLRRRNQQLE
          S..L.NLHSL.RST...EL.LD.G...T...AGQSL..ENGQWI..T.I..G.D.R.E.......NQ.LE
Retrocopy SQPL*NLHSLNRSTQENELDLDFGS<STIIQAGQSLTSENGQWISDTWIGEGTDGR<ET*HIHGQNQRLE

Parental  EENNLLRLKVDILLDMLSETTAESHLMEKELDELKSINRRR
          E.NN.L.LKVDILL.M...TT.E.HLM.KE.D.LKS...RR
Retrocopy ETNNQL*LKVDILLNMQPGTTVELHLMGKE*DKLKSFTSRR

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	2.92 RPM
SRP012922_cerebellum	0.00 RPM	11.27 RPM
SRP012922_heart	0.00 RPM	3.71 RPM
SRP012922_kidney	0.00 RPM	5.75 RPM
SRP012922_liver	0.00 RPM	1.24 RPM
SRP012922_lung	0.00 RPM	6.11 RPM
SRP012922_quadricep_muscle	0.00 RPM	2.25 RPM
SRP012922_spleen	0.00 RPM	4.81 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_875 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001384	2 retrocopies	retro_cfam_1396, retro_cfam_852,
Dasypus novemcinctus	ENSDNOG00000010982	1 retrocopy	retro_dnov_875 ,
Homo sapiens	ENSG00000100211	1 retrocopy	retro_hsap_2344,
Gorilla gorilla	ENSGGOG00000013226	1 retrocopy	retro_ggor_1781,
Myotis lucifugus	ENSMLUG00000003757	2 retrocopies	retro_mluc_1128, retro_mluc_2608,
Mustela putorius furo	ENSMPUG00000013150	1 retrocopy	retro_mputfur_1186,
Nomascus leucogenys	ENSNLEG00000015153	1 retrocopy	retro_nleu_349,
Otolemur garnettii	ENSOGAG00000028533	1 retrocopy	retro_ogar_1072,
Pan troglodytes	ENSPTRG00000014373	1 retrocopy	retro_ptro_1716,
Vicugna pacos	ENSVPAG00000001484	1 retrocopy	retro_vpac_57,