RetrogeneDB ID: retro_dnov_751

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_104558:2655..3050(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CIDEC
• Ensembl ID: ENSDNOG00000018422
• Aliases: None
• Description: cell death-inducing DFFA-like effector c [Source:HGNC Symbol;Acc:24229]

Sequence

>retro_dnov_751
TTCATGGTGCTCCAGAAGGGGCAAAAATGCCAGCTCCCATCAGAGTAGGGGAATAGGAACCATCTCTCCCTCTCCCATAA
GCCAGTCAAGAAGATCAATATGGCCTGTGTACAGTTCAGTTTGTGCAAGTTGAACCTGCAGGACTTCATTGGCTGCCTGA
GAGTCAAGGTGACGCTCTATGGCACATACTTCCTCTCGTATGATGTGTACTGCTATGGAGCCAAGTGCATCATGAAGAAA
GCCCTTCAATGGGCCCTCATAACATGCAGGCTACAGGCACATGCTGCTTGGCCCCTCCTATTACATGTAGTATCTCCTGG
ATAACACAGAGGAAGGGCAGCCCTTTCAAGGGCAAGGCCTCATTTATCATCCTGACCTGTCTGAAGATGCTGCAA

Alignment

ORF - retro_dnov_751 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 58.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FMVLQKGQKWQPLSE-GNGN---LSHK--QKIDVVGVTFILYKLNPQDFIGCLNVKATLYGTYSLSYDLH
          FMVLQKGQK.Q..SE.GN.N...LSHK...KI....V.F.L.KLN.QDFIGCL.VK.TLYGTY.LSYD..
Retrocopy FMVLQKGQKCQLPSE*GNRNHLSLSHKPVKKINMACVQFSLCKLNLQDFIGCLRVKVTLYGTYFLSYDVY

Parental  CCGAKRVVKEALRWALF-SMQATG-HVLLGTSCYMQRLLDATEEGQ-PPKGKASPLIPTCLKMLQ
          C.GAK...K.AL.WAL...MQATG.H.LLG.S.YM..LLD.TEEGQ.P.KGKAS..I.TCLKMLQ
Retrocopy CYGAKCIMKKALQWALI<NMQATG<HMLLGPSYYM*YLLDNTEEGQ>PFKGKASFIILTCLKMLQ

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	29.75 RPM
SRP012922_cerebellum	0.00 RPM	0.00 RPM
SRP012922_heart	0.00 RPM	0.23 RPM
SRP012922_kidney	0.00 RPM	32.58 RPM
SRP012922_liver	0.00 RPM	27.71 RPM
SRP012922_lung	0.00 RPM	0.00 RPM
SRP012922_quadricep_muscle	0.00 RPM	7.10 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_751 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005266	1 retrocopy	retro_cfam_293,
Dasypus novemcinctus	ENSDNOG00000018422	2 retrocopies	retro_dnov_1559, retro_dnov_751 ,
Vicugna pacos	ENSVPAG00000002888	1 retrocopy	retro_vpac_132,