RetrogeneDB ID: retro_dnov_2629

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_92132:6367..7135(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNI2
• Ensembl ID: ENSDNOG00000001502
• Aliases: None
• Description: cyclin I family, member 2 [Source:HGNC Symbol;Acc:33869]

Sequence

>retro_dnov_2629
CCTGCCGGGCAGCCGTCCCAGGAAAGACGCTGGCCGATGCCGTGCGACTGGAGAGGCTTCATGGACCAGGGCCGAGTGGT
CGCCCACCTAGACCTAGCCCTGGGCCGCGAGACGCGCCTGTGGCGGGGTGGCGAACTCCAGCAAGTCGAGATCCGCAATG
CCTTCCAGGAAGTCGTGCTGTGGCTTCTGAGGCTTGACAACATCTTTGGCTTCTCTGGGGCCACTTTTAACTTGGCTCTC
ACCGTCATCAGCTGCCTCTTGGCCTCAAGGAAGATAAAAGAGAGATACCTCAAGTGCATCACAATTACTTCCTTGAGACT
CGCTGCAAAAGTTAATGAAGAAGAAGAGTTAATTCCACGTGTAAAAGACTTCATAAAGCACTATGGTTCTGCCTATACCC
CGAATGAGCTGCTGAGGATGGAGCTGGCTATTCTGGACGTACTGCAGTGGGACCTCTATATTGGGACGCCGCTGGACTTC
TTGACTATATTCCACGCCCTGGTGGTCCTGGGCTGGCCCCACGTGTTGGACCTGCTGCCTCAGAGGAATCCTTCCCTCCA
CGTCGCGTCCCTGACCAGGCAGCTGCAGCACTGTATGGCGGGCCACCAGCTGCTGCAGTTCAAGGGCTCCACACTGGCCT
TGGTCATCATCACCTTAGAGCTGGAGAGGCTCATGCCCGACTGGTTGACTCCTACATCTGATCTGCTAAAGAAAGCACAG
ATCAGTATTGACCAGTTCAGTGACTGCAAGAAAGTTGTAACGCAGCAG

Alignment

ORF - retro_dnov_2629 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.83 %
• Parental protein coverage: 73.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PAGQPSQERRWPMPCDWRGFMDQGRVVAHLDLALGRETRLWRGGELQ-VEIRSAFQEVVLWLLRLDNIFG
          PAGQPSQERRWPMPCDWRGFMDQGRVVAHLDLALGRETRLWRGGELQ.VEIR.AFQEVVLWLLRLDNIFG
Retrocopy PAGQPSQERRWPMPCDWRGFMDQGRVVAHLDLALGRETRLWRGGELQQVEIRNAFQEVVLWLLRLDNIFG

Parental  FSGATFNLALTVISRLLASRKIKERYLKCITITSLRLAAKVNEEEELIPRVKDFIKHYGSAYTPNELLRM
          FSGATFNLALTVIS.LLASRKIKERYLKCITITSLRLAAKVNEEEELIPRVKDFIKHYGSAYTPNELLRM
Retrocopy FSGATFNLALTVISCLLASRKIKERYLKCITITSLRLAAKVNEEEELIPRVKDFIKHYGSAYTPNELLRM

Parental  ELAILDVLQWDLYIGTPLDFLTIFHALVVLGWPHVLDLLPQRNPSLHVASLTRQLQHCMAGHQLLQFKGS
          ELAILDVLQWDLYIGTPLDFLTIFHALVVLGWPHVLDLLPQRNPSLHVASLTRQLQHCMAGHQLLQFKGS
Retrocopy ELAILDVLQWDLYIGTPLDFLTIFHALVVLGWPHVLDLLPQRNPSLHVASLTRQLQHCMAGHQLLQFKGS

Parental  TLALVIITLELERLMPDWLTPTSDLLKKAQISIDQFSDCKKVVTQQ
          TLALVIITLELERLMPDWLTPTSDLLKKAQISIDQFSDCKKVVTQQ
Retrocopy TLALVIITLELERLMPDWLTPTSDLLKKAQISIDQFSDCKKVVTQQ

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	0.58 RPM
SRP012922_cerebellum	0.00 RPM	20.48 RPM
SRP012922_heart	0.00 RPM	0.93 RPM
SRP012922_kidney	0.00 RPM	0.00 RPM
SRP012922_liver	0.00 RPM	0.00 RPM
SRP012922_lung	0.00 RPM	1.22 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.35 RPM
SRP012922_spleen	0.00 RPM	1.95 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_2629 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000600	1 retrocopy	retro_chof_1457,
Callithrix jacchus	ENSCJAG00000013222	1 retrocopy	retro_cjac_3834,
Dasypus novemcinctus	ENSDNOG00000001502	1 retrocopy	retro_dnov_2629 ,
Dasypus novemcinctus	ENSDNOG00000005210	1 retrocopy	retro_dnov_2498,
Dasypus novemcinctus	ENSDNOG00000015166	1 retrocopy	retro_dnov_1275,