RetrogeneDB ID: retro_dnov_1510

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_2207:115730..116038(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FABP3
• Ensembl ID: ENSDNOG00000000511
• Aliases: None
• Description: fatty acid binding protein 3, muscle and heart (mammary-derived growth inhibitor) [Source:HGNC Symbol;Acc:3557]

Sequence

>retro_dnov_1510
ATAGATTTTGCTACTGGGCAGGTGGCTGCCATGACCAAGACTACCACAATCATTGGAAAAATGGGGACAGCATCAACACA
AAAGTACAGAGCACCTTCAAGAACATGGAGATCAGCATCAAGGTAAGTGTATAGTTTGATGAGACAACAGCAGGTGACAG
GAAAGTAAATCGTACTGTGACATTTGAAGGAGGCAATTTCCATGTATAGAAGTGGGACAGGCAAGAGATGGCATTTGTGC
AGGAGCTAAATCATGGTAAACTCATCCTGATACTCACATGTGGCAGTACTCGTACTTATTAGAAAGAG

Alignment

ORF - retro_dnov_1510 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.41 %
• Parental protein coverage: 99.07 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VGFAIRQVGAMTKPFTIIEQ-NGDTITIKTQSTFKSTEISFQLGVEFDETTADDRKVKSIVTLDGGKLVH
          ..FA..QV.AMTK..TII...NGD.I..K.QSTFK..EIS....V.FDETTA.DRKV...VT..GG...H
Retrocopy IDFATGQVAAMTKTTTIIGK<NGDSINTKVQSTFKNMEISIKVSV*FDETTAGDRKVNRTVTFEGGNF-H

Parental  VQKWNGQETTLVRELKDGKLILTLTLGNVVSTRIYEKE
          V.KW..QE...V.EL..GKLIL.LT.G...STR.Y.KE
Retrocopy V*KWDRQEMAFVQELNHGKLILILTCG---STRTY*KE

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	29.17 RPM
SRP012922_cerebellum	0.00 RPM	18.15 RPM
SRP012922_heart	0.00 RPM	761.99 RPM
SRP012922_kidney	0.27 RPM	47.64 RPM
SRP012922_liver	0.00 RPM	0.15 RPM
SRP012922_lung	0.00 RPM	7.94 RPM
SRP012922_quadricep_muscle	0.00 RPM	656.68 RPM
SRP012922_spleen	0.00 RPM	0.92 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_1510 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 17 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016819	2 retrocopies	retro_btau_1467, retro_btau_295,
Danio rerio	ENSDARG00000023290	1 retrocopy	retro_drer_33,
Dasypus novemcinctus	ENSDNOG00000000511	2 retrocopies	retro_dnov_1510 , retro_dnov_2482,
Dasypus novemcinctus	ENSDNOG00000018066	5 retrocopies	retro_dnov_1073, retro_dnov_1231, retro_dnov_1318, retro_dnov_2392, retro_dnov_559,
Equus caballus	ENSECAG00000024852	1 retrocopy	retro_ecab_519,
Homo sapiens	ENSG00000121769	1 retrocopy	retro_hsap_1258,
Gorilla gorilla	ENSGGOG00000014432	1 retrocopy	retro_ggor_990,
Macropus eugenii	ENSMEUG00000012501	6 retrocopies	retro_meug_1037, retro_meug_148, retro_meug_1660, retro_meug_273, retro_meug_563, retro_meug_819,
Microcebus murinus	ENSMICG00000009359	4 retrocopies	retro_mmur_1490, retro_mmur_203, retro_mmur_621, retro_mmur_734,
Myotis lucifugus	ENSMLUG00000013609	2 retrocopies	retro_mluc_1144, retro_mluc_1717,
Mus musculus	ENSMUSG00000028773	3 retrocopies	retro_mmus_2804, retro_mmus_3204, retro_mmus_65,
Nomascus leucogenys	ENSNLEG00000001586	1 retrocopy	retro_nleu_2097,
Otolemur garnettii	ENSOGAG00000013757	4 retrocopies	retro_ogar_1148, retro_ogar_1312, retro_ogar_1873, retro_ogar_959,
Pongo abelii	ENSPPYG00000001616	1 retrocopy	retro_pabe_1048,
Pan troglodytes	ENSPTRG00000000457	1 retrocopy	retro_ptro_3047,
Rattus norvegicus	ENSRNOG00000012879	1 retrocopy	retro_rnor_2199,
Ictidomys tridecemlineatus	ENSSTOG00000003842	3 retrocopies	retro_itri_1544, retro_itri_640, retro_itri_641,