RetrogeneDB ID: retro_dnov_2592

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_8878:30867..31185(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATPIF1
• Ensembl ID: ENSDNOG00000015460
• Aliases: None
• Description: ATPase inhibitory factor 1 [Source:HGNC Symbol;Acc:871]

Sequence

>retro_dnov_2592
ATGGCAGTTTCGACCTTGGGTTCGCGTATGCGGCTCGGCGTGTGGGGCGTAAGGGCCATGCAAGGCCGAAGCTTCCGCTC
GGACCAGTCAGACCAAGTCCACGGAAGCGCTGGCTCAGTTCGGGAGGCCGGTGGGGCCTTCGGAAAAAGAGAGGCGTCAG
AAGAGGAGCGATACTTCCGAGAGCAGACCAGAAAACAACTGGCAGCCTTGAAGAAACACCATGAAGATGAGATCGTTTAT
TCTAAGAAAGAGATTGAGCGTCTGCAGAAAGAAATGGAGCGGCACAAGCAGAAGATCAAGAAACTAAACTATGATGAT

Alignment

ORF - retro_dnov_2592 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.23 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVSTLGSRMRLGVWGVRAMQGRSFGSDQSDQVHGSAGSVREAGGAFGKREAAEEERYFREQTRKQLAAL
          MAVSTLGSRMRLGVWGVRAMQGRSF.SDQSDQVHGSAGSVREAGGAFGKREA.EEERYFREQTRKQLAAL
Retrocopy MAVSTLGSRMRLGVWGVRAMQGRSFRSDQSDQVHGSAGSVREAGGAFGKREASEEERYFREQTRKQLAAL

Parental  KKHHEDEIVYSKKEIERLQKEIERHKQKIKKLNHDD
          KKHHEDEIVYSKKEIERLQKE.ERHKQKIKKLN.DD
Retrocopy KKHHEDEIVYSKKEIERLQKEMERHKQKIKKLNYDD

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	45.89 RPM	323.01 RPM
SRP012922_cerebellum	21.17 RPM	160.84 RPM
SRP012922_heart	58.01 RPM	519.29 RPM
SRP012922_kidney	33.13 RPM	291.04 RPM
SRP012922_liver	15.02 RPM	118.12 RPM
SRP012922_lung	16.19 RPM	124.47 RPM
SRP012922_quadricep_muscle	46.39 RPM	358.80 RPM
SRP012922_spleen	20.26 RPM	126.82 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_2592 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032458	2 retrocopies	retro_cfam_1777, retro_cfam_651,
Callithrix jacchus	ENSCJAG00000009581	1 retrocopy	retro_cjac_1406,
Dasypus novemcinctus	ENSDNOG00000015460	1 retrocopy	retro_dnov_2592 ,
Myotis lucifugus	ENSMLUG00000000170	1 retrocopy	retro_mluc_363,
Mustela putorius furo	ENSMPUG00000015536	1 retrocopy	retro_mputfur_1570,
Mus musculus	ENSMUSG00000054428	2 retrocopies	retro_mmus_2516, retro_mmus_908,
Otolemur garnettii	ENSOGAG00000010337	2 retrocopies	retro_ogar_116, retro_ogar_268,
Pteropus vampyrus	ENSPVAG00000017615	1 retrocopy	retro_pvam_817,
Rattus norvegicus	ENSRNOG00000013300	1 retrocopy	retro_rnor_2655,
Sorex araneus	ENSSARG00000010860	1 retrocopy	retro_sara_458,
Ictidomys tridecemlineatus	ENSSTOG00000020766	1 retrocopy	retro_itri_1240,