RetrogeneDB ID: retro_dnov_2559

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_85603:3804..4464(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHCHD3
• Ensembl ID: ENSDNOG00000004942
• Aliases: None
• Description: coiled-coil-helix-coiled-coil-helix domain containing 3 [Source:HGNC Symbol;Acc:21906]

Sequence

>retro_dnov_2559
ATGGGCGGTGCAGGCAGCACCCGCCGGGTCACCTTCGAGGCAGACGAGAATGAGAACATCACCGTAGTGAAGGGCATCCG
GCTTTCAGAAAATGTGATTGATCGAATGAAGGAGTCCTCTCCATCTGGTTCGAAGCCTCAGCGATATTCTAGTGCTTATG
GAGCCTCAGTTCCTGAAGAAGAATTGAAAAGAAGAGTAGCTGAGGAGCTAGCATTGGAACAAGCCAAGAAAGAATCTGAA
AATAAAAAACGACTGAAGCAAAGCAAAGAACTGGACCAAGAAAGGGCTGCTGCCAGTGAGCAGTTAACCAGAGCTATTCT
ACGAGAGAGAATATCAAGTGAGGAGGAACGCTCTAAGGCAAGGCATCTGGCCAAGCAGCTGGAAGAGAGAGACTGAGTGA
TAAAGAAGCAGGATGCGTTCTACAAAGAGCAGCTGGCTAGACTGGAGGAGAGGAGTTCAGAATTCTACAAAGTCACCACC
GAGCAATATCAGAAAGCTGCTGAAGAAGTGGAAGCAAAGTTCAAGCGGTATGAGTTTCACCCAGTCTGTGCCGATCTGCA
GGCCAAAATTCTCCAGTGTTACCGCCAGAACACCCAGCAGACCCTCAGCTGCTCTGCTCTGGCCAGCCAGTACATGCACT
GTGTCAATCATGCTAAACAG

Alignment

ORF - retro_dnov_2559 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGGAGSTRRVTFEADENENITVVKGIRLSENVIDRMKESSPSGSKPQRYSSGYGASVSEEELKRRVAEEL
          MGGAGSTRRVTFEADENENITVVKGIRLSENVIDRMKESSPSGSKPQRYSS.YGASV.EEELKRRVAEEL
Retrocopy MGGAGSTRRVTFEADENENITVVKGIRLSENVIDRMKESSPSGSKPQRYSSAYGASVPEEELKRRVAEEL

Parental  ALEQAKKESENKKRLKQSKELDQERAAASEQLTRAILRERISSEEERSKAKHLAKQLEERDRVIKKQEAF
          ALEQAKKESENKKRLKQSKELDQERAAASEQLTRAILRERISSEEERSKA.HLAKQLEERD.VIKKQ.AF
Retrocopy ALEQAKKESENKKRLKQSKELDQERAAASEQLTRAILRERISSEEERSKARHLAKQLEERD*VIKKQDAF

Parental  YKEQLARLXXXSSEFYKVTTEQYQKAAEEVEAKFKRYEFHPVCADLQAKILQCYRQNTQQTLSCSALASQ
          YKEQLARL...SSEFYKVTTEQYQKAAEEVEAKFKRYEFHPVCADLQAKILQCYRQNTQQTLSCSALASQ
Retrocopy YKEQLARLEERSSEFYKVTTEQYQKAAEEVEAKFKRYEFHPVCADLQAKILQCYRQNTQQTLSCSALASQ

Parental  YMHCVNHAKQ
          YMHCVNHAKQ
Retrocopy YMHCVNHAKQ

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	45.51 RPM	48.23 RPM
SRP012922_cerebellum	31.07 RPM	22.82 RPM
SRP012922_heart	109.98 RPM	69.61 RPM
SRP012922_kidney	42.71 RPM	32.03 RPM
SRP012922_liver	16.25 RPM	10.68 RPM
SRP012922_lung	22.91 RPM	20.77 RPM
SRP012922_quadricep_muscle	115.10 RPM	75.29 RPM
SRP012922_spleen	41.43 RPM	33.88 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_2559 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 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001312	1 retrocopy	retro_cfam_374,
Dasypus novemcinctus	ENSDNOG00000004942	1 retrocopy	retro_dnov_2559 ,
Homo sapiens	ENSG00000106554	3 retrocopies	retro_hsap_358, retro_hsap_3759, retro_hsap_542,
Macaca mulatta	ENSMMUG00000001671	1 retrocopy	retro_mmul_14,
Mus musculus	ENSMUSG00000053768	1 retrocopy	retro_mmus_3452,
Nomascus leucogenys	ENSNLEG00000012967	3 retrocopies	retro_nleu_168, retro_nleu_716, retro_nleu_904,
Oryctolagus cuniculus	ENSOCUG00000014032	1 retrocopy	retro_ocun_801,
Pongo abelii	ENSPPYG00000025827	5 retrocopies	retro_pabe_2492, retro_pabe_3161, retro_pabe_345, retro_pabe_411, retro_pabe_501,
Pan troglodytes	ENSPTRG00000019711	4 retrocopies	retro_ptro_2550, retro_ptro_282, retro_ptro_407, retro_ptro_701,
Rattus norvegicus	ENSRNOG00000013211	1 retrocopy	retro_rnor_2874,
Sorex araneus	ENSSARG00000012111	1 retrocopy	retro_sara_592,
Ictidomys tridecemlineatus	ENSSTOG00000022282	1 retrocopy	retro_itri_1301,