RetrogeneDB ID: retro_dnov_2463

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_77250:47002..47353(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C16orf87
• Ensembl ID: ENSDNOG00000006412
• Aliases: None
• Description: chromosome 16 open reading frame 87 [Source:HGNC Symbol;Acc:33754]

Sequence

>retro_dnov_2463
AACAGAAAACTTTTAAATGCAAAACATTCAGAGAAATCACAACCTTCTACAGAAAAACAAGTGTGAGGCCAAGAGGAGCC
AAATGGAGAGAGTTAGGCAAGAGAAGTTAAATTCTACTGTAAATAAGGATTTAGAAAAAGAAAGAGGTCTCAGAGTAACA
GCCATTCAGATCATATCAGATGAGGAAGAGAAAGACCTAAAGGTGCATTTGCCAACAGACATGAGGAAGAAATAGAGAAA
GAGGAAAAGGAAATTGACACCTATGCTAACCTCACTGATAAAAAGGCTTTAGTGTTTTCAGTCACCTTGGTAGAAAAAAA
TAGAAAAATTATCAATCAAAGACTTATTCTA

Alignment

ORF - retro_dnov_2463 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.47 %
• Parental protein coverage: 75.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SRKLLNARHSEKSPPSTE-NKHEAKRRRTERVRREKINSTVNKDLE-NRKRSRSNSHSDHIRRGRGRPKS
          .RKLLNA.HSEKS.PSTE.NK.EAKR...ERVR.EK.NSTVNKDLE..RKRS.SNSHSDHIR.GR.RPK.
Retrocopy NRKLLNAKHSEKSQPSTE>NKCEAKRSQMERVRQEKLNSTVNKDLE<KRKRSQSNSHSDHIR*GRERPKG

Parental  ASAKKHEEEREKQEKEIDIYANLSDEKAFVFSVALAEINRKIINQRLIL
          A.A..HEEE.EK.EKEID.YANL.D.KA.VFSV.L.E.NRKIINQRLIL
Retrocopy AFANRHEEEIEKEEKEIDTYANLTDKKALVFSVTLVEKNRKIINQRLIL

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	8.94 RPM
SRP012922_heart	0.00 RPM	3.71 RPM
SRP012922_kidney	0.00 RPM	2.46 RPM
SRP012922_liver	0.00 RPM	2.32 RPM
SRP012922_lung	0.00 RPM	7.03 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.73 RPM
SRP012922_spleen	0.00 RPM	5.72 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_2463 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003679	1 retrocopy	retro_cfam_1054,
Cavia porcellus	ENSCPOG00000010228	2 retrocopies	retro_cpor_1197, retro_cpor_1228,
Dasypus novemcinctus	ENSDNOG00000006412	2 retrocopies	retro_dnov_1512, retro_dnov_2463 ,
Tupaia belangeri	ENSTBEG00000013316	2 retrocopies	retro_tbel_3011, retro_tbel_305,
Tarsius syrichta	ENSTSYG00000008921	1 retrocopy	retro_tsyr_1758,