RetrogeneDB ID: retro_dnov_232

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_2848:116164..116543(+)
• Located in intron of: ENSDNOG00000011197

Retrocopy information

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

Parental gene information

• Parental gene symbol: C12orf49
• Ensembl ID: ENSDNOG00000001294
• Aliases: None
• Description: chromosome 12 open reading frame 49 [Source:HGNC Symbol;Acc:26128]

Sequence

>retro_dnov_232
GAGGAGAGGGCAGTGAGAGATTGGAATCTTCTCTAGGTTCAAGACCATGATCAACCTATTCCCTGGAAAGTGAAGTTTAA
TCTGGGCAATAGCAGTCGACCAGGCAATCGATGCTGTAACTTCATTCAAGGGAAGTACTTAATCACGGAAGAACTAGGAT
ACATTTGTGAGAGGAAGGATTTCCTGGTGACAACTGCTGTCATTTCCACATCCCTAACACAAAGCAATAACTTGTGATGG
CTGTTTGTCCAATGACTGATGTAGCACCTATGAGTATTGTGTCTCTGCTGCCTGCAGCCCAACAGGAAACTTCTGGAGAG
CTTCTCTCAGCTGGGCAGCCATGGCATTCCAGAACCTCTTAATGGCAGTGGAAGATCAC

Alignment

ORF - retro_dnov_232 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.52 %
• Parental protein coverage: 76.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EERAVRDRNLLQVQDHDQPIPWKVQFNLGNSSRPGNQCRNSIQGKHLITDELGYVCERKDLLV-NGCCHV
          EERAVRD.NLL.VQDHDQPIPWKV.FNLGNSSRPGN.C.N.IQGK.LIT.ELGY.CERKD.LV...CCH.
Retrocopy EERAVRDWNLL*VQDHDQPIPWKVKFNLGNSSRPGNRCCNFIQGKYLITEELGYICERKDFLV<DNCCHF

Parental  HVPSTKQ-YCCDGCLSNGCCSAYEYCVS-CCLQPNKQLLLERF-LNRAAMAFQNLFMAVEDH
          H.P.TKQ...CDGCLSN..CS.YEYCVS.CCLQPN...LLE.F.L..AAMAFQNL.MAVEDH
Retrocopy HIPNTKQ<ITCDGCLSND*CSTYEYCVS<CCLQPNRK-LLESF>LSWAAMAFQNLLMAVEDH

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	0.39 RPM	2.14 RPM
SRP012922_cerebellum	0.14 RPM	3.85 RPM
SRP012922_heart	0.00 RPM	0.00 RPM
SRP012922_kidney	0.00 RPM	4.11 RPM
SRP012922_liver	0.00 RPM	2.01 RPM
SRP012922_lung	0.00 RPM	2.60 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.87 RPM
SRP012922_spleen	0.00 RPM	2.63 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_232 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 10 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012481	2 retrocopies	retro_amel_1518, retro_amel_1578,
Bos taurus	ENSBTAG00000047139	1 retrocopy	retro_btau_1667,
Callithrix jacchus	ENSCJAG00000009570	1 retrocopy	retro_cjac_1471,
Dasypus novemcinctus	ENSDNOG00000001294	9 retrocopies	retro_dnov_126, retro_dnov_1532, retro_dnov_1609, retro_dnov_1622, retro_dnov_1739, retro_dnov_2042, retro_dnov_2185, retro_dnov_2285, retro_dnov_232 ,
Echinops telfairi	ENSETEG00000016892	3 retrocopies	retro_etel_1064, retro_etel_1377, retro_etel_410,
Homo sapiens	ENSG00000111412	1 retrocopy	retro_hsap_4758,
Gorilla gorilla	ENSGGOG00000015690	2 retrocopies	retro_ggor_2963, retro_ggor_508,
Myotis lucifugus	ENSMLUG00000011912	1 retrocopy	retro_mluc_166,
Macaca mulatta	ENSMMUG00000018247	2 retrocopies	retro_mmul_2376, retro_mmul_2537,
Pan troglodytes	ENSPTRG00000005500	1 retrocopy	retro_ptro_2798,