RetrogeneDB ID: retro_dnov_2175

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_52879:28..674(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000007283
• Aliases: None
• Description: None

Sequence

>retro_dnov_2175
AGTGATGATTCTGACATTTAAGATAACACAATATTGATAAAAGCCTATGATAAAGCTGTGGCTTCATTTAAGCATGCTCT
GAAGAATGGTGACATTTCTCAAATTTCAGACAAACCAAAAGGCACACCTAAAAGAAAACCTGTTAAGAAGAATAAAAGCC
AAAAAAAGAACATCACAACTCCAATAAAACAGTGGAAAGTTGGTGACAAATGTTCTGCCATTTGGTCAGAAGATGGCTAC
ATTTACTCAGCTACCATTGCTTCAATTGACTTTAAGAGAGAGATCTGTGCTGTGGTGTACACTGGGTATGGAAAAGTAGA
GGAGCAAAATCTGTCTCATTTACTTTTCCCAACCTTTGAAGGAGTTAATAACGCAGAACAAAGTGCTCAGGAGAATGAAC
CTAAGAGTCAACTTTCAACAGATGAAAGTGAGAACGCTTCCCAAGTCTCCTGGAAATAAACTAAACAACAAAAGTCAAAA
GCTACTCCATGGAACTCTTTTCTGCTTGTACACCCCATCCCCCCATGCCAGGATCAGGACTGGGAGCAGGAAAGTCAGGC
CTAAAATTGACTGCCCTCCCCCCTTCCTGTCCTGCTGGCTGCCTCCACTTCCTTCTGGACCACCAATACTTCCCCTTCCT
CGTCCC

Alignment

ORF - retro_dnov_2175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.09 %
• Parental protein coverage: 79.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SDDSDIWDDTALIKAYDKAVASFKHALKNGDISEVSNKPKGTPKRKPVKKNKSQKKNITTPLKQWKVGDK
          SDDSDI.D.T.LIKAYDKAVASFKHALKNGDIS..S.KPKGTPKRKPVKKNKSQKKNITTP.KQWKVGDK
Retrocopy SDDSDI*DNTILIKAYDKAVASFKHALKNGDISQISDKPKGTPKRKPVKKNKSQKKNITTPIKQWKVGDK

Parental  CSAIWSEDGCIYPATIASIDFKRDTCVVVYTGYGNREEQNLSDLLFPTFEGVNNVEQNAQENENESQLST
          CSAIWSEDG.IY.ATIASIDFKR..C.VVYTGYG..EEQNLS.LLFPTFEGVNN.EQ.AQENE..SQLST
Retrocopy CSAIWSEDGYIYSATIASIDFKREICAVVYTGYGKVEEQNLSHLLFPTFEGVNNAEQSAQENEPKSQLST

Parental  DESENSS-KSPGNKPNNIKSKATTWNSFLPPPPPMPGSGLGPGKSGLKFNGPPPPPPPPFLSCWLPPLPS
          DESEN.S.KSPGNK.NN.KS.............P.P......G........P....PPPFLSCWLPPLPS
Retrocopy DESENAS>KSPGNKLNN-KSQKLLHGTLFCLYTPSPHARIRTGSRKVR---PKIDCPPPFLSCWLPPLPS

Parental  GPPILPPPPP
          GPPILP.P.P
Retrocopy GPPILPLPRP

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	15.56 RPM
SRP012922_cerebellum	0.41 RPM	15.26 RPM
SRP012922_heart	0.00 RPM	7.66 RPM
SRP012922_kidney	0.00 RPM	8.76 RPM
SRP012922_liver	0.00 RPM	5.88 RPM
SRP012922_lung	0.00 RPM	11.61 RPM
SRP012922_quadricep_muscle	0.00 RPM	6.40 RPM
SRP012922_spleen	0.11 RPM	14.77 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_2175 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 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000012328	1 retrocopy	retro_cpor_988,
Dasypus novemcinctus	ENSDNOG00000007283	4 retrocopies	retro_dnov_1239, retro_dnov_1613, retro_dnov_1637, retro_dnov_2175 ,
Echinops telfairi	ENSETEG00000001406	2 retrocopies	retro_etel_1549, retro_etel_2012,
Homo sapiens	ENSG00000205571	1 retrocopy	retro_hsap_4140,
Gorilla gorilla	ENSGGOG00000026704	1 retrocopy	retro_ggor_2780,
Myotis lucifugus	ENSMLUG00000010603	1 retrocopy	retro_mluc_1623,
Macaca mulatta	ENSMMUG00000020214	1 retrocopy	retro_mmul_216,
Nomascus leucogenys	ENSNLEG00000004454	1 retrocopy	retro_nleu_1054,
Oryctolagus cuniculus	ENSOCUG00000017097	1 retrocopy	retro_ocun_617,
Pan troglodytes	ENSPTRG00000016955	1 retrocopy	retro_ptro_2813,
Sus scrofa	ENSSSCG00000016970	1 retrocopy	retro_sscr_654,
Ictidomys tridecemlineatus	ENSSTOG00000012288	1 retrocopy	retro_itri_968,
Tupaia belangeri	ENSTBEG00000002399	1 retrocopy	retro_tbel_1033,