RetrogeneDB ID: retro_dnov_1033

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_138252:3885..4194(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC59
• Ensembl ID: ENSDNOG00000011546
• Aliases: None
• Description: coiled-coil domain containing 59 [Source:HGNC Symbol;Acc:25005]

Sequence

>retro_dnov_1033
TCAGAAGAGCAAGTTGACCAGCCTTTGCCACAAGTACCGTGTAGCACTGACCAGCCTCTACCAGCAGGGAAACATATAGA
GAAAAAGAAAATATCAAATCAAAAAGCATAAGATGAATATGAACAGGCTCAAGCAAACTAGCTGCTAAGAAAGAACTTGA
GAGAAGAAAACGAAATACGCTCAGAGGTGCCATAAAAAAAAAAAAAAAAGAAAATGGAAGTTTTCAAAGTGTTGTGCAAA
AAGACTGAAAAGGGCCAACTAAACTTGACTTTACAAATGGAGTATCTCCTTCCAAAAGTACAAGAAAAA

Alignment

ORF - retro_dnov_1033 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.56 %
• Parental protein coverage: 53. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SEEQCSIDRTLPAEQCSKTVNSTAISKKNKKKTSNQKAQEEYEQVQA-KRAAKKQEFERRKRE-REESQR
          SEEQ...D..LP...CS......A.....KKK.SNQKA..EYEQ.QA.K.AAKK.E.ERRKR..R.E...
Retrocopy SEEQ--VDQPLPQVPCSTDQPLPAGKHIEKKKISNQKA*DEYEQAQA<KLAAKK-ELERRKRN>RSEVPX

Parental  LYKKKKMEMFKILSKKTKKGQPNLNLQMEYLLQKIQEK
          .......E.FK.L.KKT.KGQ.NL.LQMEYLL.K.QEK
Retrocopy XXXXXXXEVFKVLCKKTEKGQLNLTLQMEYLLPKVQEK

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	16.72 RPM
SRP012922_cerebellum	0.00 RPM	20.76 RPM
SRP012922_heart	0.00 RPM	8.59 RPM
SRP012922_kidney	0.00 RPM	18.34 RPM
SRP012922_liver	0.00 RPM	7.90 RPM
SRP012922_lung	0.00 RPM	27.49 RPM
SRP012922_quadricep_muscle	0.00 RPM	8.13 RPM
SRP012922_spleen	0.00 RPM	23.58 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_1033 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 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016875	1 retrocopy	retro_amel_954,
Bos taurus	ENSBTAG00000036282	4 retrocopies	retro_btau_725, retro_btau_726, retro_btau_727, retro_btau_728,
Choloepus hoffmanni	ENSCHOG00000007788	1 retrocopy	retro_chof_1648,
Dasypus novemcinctus	ENSDNOG00000011546	1 retrocopy	retro_dnov_1033 ,
Dipodomys ordii	ENSDORG00000003005	1 retrocopy	retro_dord_485,
Echinops telfairi	ENSETEG00000000256	2 retrocopies	retro_etel_1338, retro_etel_1789,
Gorilla gorilla	ENSGGOG00000025296	2 retrocopies	retro_ggor_1386, retro_ggor_99,
Microcebus murinus	ENSMICG00000000967	4 retrocopies	retro_mmur_1456, retro_mmur_354, retro_mmur_689, retro_mmur_909,
Oryctolagus cuniculus	ENSOCUG00000017824	2 retrocopies	retro_ocun_1782, retro_ocun_498,
Otolemur garnettii	ENSOGAG00000004383	1 retrocopy	retro_ogar_2065,
Pan troglodytes	ENSPTRG00000005266	1 retrocopy	retro_ptro_1270,
Tupaia belangeri	ENSTBEG00000008887	7 retrocopies	retro_tbel_1515, retro_tbel_2047, retro_tbel_2126, retro_tbel_302, retro_tbel_3391, retro_tbel_3721, retro_tbel_972,