RetrogeneDB ID: retro_dnov_950

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_126157:6694..7099(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATG5
• Ensembl ID: ENSDNOG00000013004
• Aliases: None
• Description: autophagy related 5 [Source:HGNC Symbol;Acc:589]

Sequence

>retro_dnov_950
AGTCAAGTAATCAATGAAATGTGGAAAAAAGATCATAAGCAGCTCTGGATGGGATTATAAAATGACAGGTTTGACCAGTT
TTGGGCTATCAATCAGAAATGCATGAAATATTCTGCGGAGGAAAGTGGATTTTATTACATCCCTTTTAGAATATATAAAA
CAACAATTGAATGACCTTTCATTCAGAAGCTGTTTCATCCTGTGGCTGCAGATGGACAGTTGCATACATCAGGAAATCTC
CTCAGAGAAGCTTGTCCTTCAGCAATTGCTCCTGAAGGTGGGGGAAAAAAGAATCAAGTAATGATTCATGGAATTGAGCC
AATGATGGAGACACCTTTGCAGTGGCTGAGTGAACACCTGAGCTACCCAGGTAGTTTTCTTCATTTTAGTATCATCCCAC
AACCA

Alignment

ORF - retro_dnov_950 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.44 %
• Parental protein coverage: 56.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SQVINEMQKKDHKQLWMGLQNDRFDQFWAINRKLMEYPAEENGFRYIPFRIYQTTTERPFIQKLFRPVAA
          SQVINEM.KKDHKQLWMGL.NDRFDQFWAIN.K.M.Y.AEE.GF.YIPFRIY.TT.E.PFIQKLF.PVAA
Retrocopy SQVINEMWKKDHKQLWMGL*NDRFDQFWAINQKCMKYSAEESGFYYIPFRIYKTTIE*PFIQKLFHPVAA

Parental  DGQLHTLGDLLKEVCPSAIAPEDGEKKNQVMIHGIEPMMETPLQWLSEHLSYPDNFLHVSIIPQP
          DGQLHT.G.LL.E.CPSAIAPE.G.KKNQVMIHGIEPMMETPLQWLSEHLSYP..FLH.SIIPQP
Retrocopy DGQLHTSGNLLREACPSAIAPEGGGKKNQVMIHGIEPMMETPLQWLSEHLSYPGSFLHFSIIPQP

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	10.11 RPM
SRP012922_cerebellum	0.00 RPM	3.30 RPM
SRP012922_heart	0.00 RPM	2.09 RPM
SRP012922_kidney	0.00 RPM	6.02 RPM
SRP012922_liver	0.00 RPM	7.74 RPM
SRP012922_lung	0.00 RPM	8.09 RPM
SRP012922_quadricep_muscle	0.00 RPM	3.63 RPM
SRP012922_spleen	0.00 RPM	12.48 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_950 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006399	1 retrocopy	retro_chof_1928,
Dasypus novemcinctus	ENSDNOG00000013004	2 retrocopies	retro_dnov_1805, retro_dnov_950 ,
Myotis lucifugus	ENSMLUG00000014090	1 retrocopy	retro_mluc_872,
Ictidomys tridecemlineatus	ENSSTOG00000016507	1 retrocopy	retro_itri_1724,