RetrogeneDB ID: retro_dnov_22

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_38593:50502..51051(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000019290
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FOXR1
• Ensembl ID: ENSDNOG00000009414
• Aliases: None
• Description: forkhead box R1 [Source:HGNC Symbol;Acc:29980]

Sequence

>retro_dnov_22
ATGGACTTAAAACTTAAAAATCTTGAATTTTGGTACAGTCTCCATGGGCAGGTTCCAGGGCTGCTGGACTGGGACATGGG
AAATGAATTTTTCTTGCCCCACACCACAGACCAGCACCCCTTAGCTGAACAGAACCTTGCTAAATACCAACTCCAAATAA
TGGAATCCCCAAAGCTGCCTCTGGAGAGGAGACCCAATCCTGACAAGGATGGTCCTGACTATGACCCCAATCTGTGGATG
TGGGTGAACCCCAACATAGTGTGCTCCCTCAGCATCCAGGAGGCCCCAAATCGCAATAAGGAAAAGGATCTGACAAGTGT
GCTTCCCTCCCTTCAGCCACCCTCAAAGGATGAAGAGTTTACTTGCTTAGAGGCCACAGTTGTGGAGTCCCTTCCATCTT
CCTCCAGCGAGCAGTACCCCCTACAAAAGCGGTTCACCTCTTTCCCCAGTGACTGGGAGCTCACAGAAGAGAAAGCTGAG
GAACAAGATGGAAACTCCTCTGCTGCCCTCCGGTCCCCTGACAAAGGGAAGTGCTACCAGAGCCAAAAA

Alignment

ORF - retro_dnov_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.9 %
• Parental protein coverage: 51.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ARYRLRLVKPPKLPLEKKPRPDRDGPDIEPNLWMWVNSNIVYPPGKLEAAAR---EALTSTL-CPQPPPK
          A.Y.L.....PKLPLE..P.PD.DGPD..PNLWMWVN.NIV......EA..R.....LTS.L...QPP.K
Retrocopy AKYQLQIMESPKLPLERRPNPDKDGPDYDPNLWMWVNPNIVCSLSIQEAPNRNKEKDLTSVLPSLQPPSK

Parental  EEESSCPKVTVVEALPPCSSEESPPGKWFASSPSDWELTEEEEAENHDDSSFGALSPPHKKGSLQSRR
          .EE..C...TVVE.LP..SSE..P..K.F.S.PSDWELT.EE.AE..D..S..AL..P.K....QS..
Retrocopy DEEFTCLEATVVESLPSSSSEQYPLQKRFTSFPSDWELT-EEKAEEQDGNSSAALRSPDKGKCYQSQK

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	0.00 RPM
SRP012922_cerebellum	0.00 RPM	0.96 RPM
SRP012922_heart	0.00 RPM	3.25 RPM
SRP012922_kidney	0.00 RPM	0.82 RPM
SRP012922_liver	0.00 RPM	0.00 RPM
SRP012922_lung	0.00 RPM	0.00 RPM
SRP012922_quadricep_muscle	0.00 RPM	3.63 RPM
SRP012922_spleen	0.00 RPM	0.11 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_22 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 18 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000053	1 retrocopy	retro_amel_39,
Bos taurus	ENSBTAG00000014606	1 retrocopy	retro_btau_189,
Canis familiaris	ENSCAFG00000012417	1 retrocopy	retro_cfam_209,
Callithrix jacchus	ENSCJAG00000013656	1 retrocopy	retro_cjac_4066,
Dasypus novemcinctus	ENSDNOG00000009414	1 retrocopy	retro_dnov_22 ,
Dipodomys ordii	ENSDORG00000001960	1 retrocopy	retro_dord_651,
Homo sapiens	ENSG00000176302	1 retrocopy	retro_hsap_72,
Microcebus murinus	ENSMICG00000002680	1 retrocopy	retro_mmur_38,
Macaca mulatta	ENSMMUG00000022722	1 retrocopy	retro_mmul_125,
Mustela putorius furo	ENSMPUG00000004890	1 retrocopy	retro_mputfur_161,
Nomascus leucogenys	ENSNLEG00000007376	1 retrocopy	retro_nleu_50,
Otolemur garnettii	ENSOGAG00000007258	1 retrocopy	retro_ogar_296,
Procavia capensis	ENSPCAG00000010132	1 retrocopy	retro_pcap_12,
Pongo abelii	ENSPPYG00000003947	1 retrocopy	retro_pabe_69,
Pan troglodytes	ENSPTRG00000004358	1 retrocopy	retro_ptro_94,
Sorex araneus	ENSSARG00000011319	1 retrocopy	retro_sara_38,
Sus scrofa	ENSSSCG00000015101	1 retrocopy	retro_sscr_36,
Ictidomys tridecemlineatus	ENSSTOG00000014321	1 retrocopy	retro_itri_158,