RetrogeneDB ID: retro_dnov_1239

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_168081:342..753(+)
• 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_1239
ATCGCAACTCCATTGAAACAGCGGAAAGTTGGTAACATTTGTTCTGCCGTTTGGTCAGAAGACAGCTGCACTCACTCAGC
TGCCATTGCTTTCATTGATTTTAAGAGTGGTAACTGTGCTGTGGTTTACACTGGGAATGGCAATAGAGAAAAGCAAAATC
TGTCTGATTTACTTTTCCCAACCTTAGAAGGAGTCAACAATGTAGAACAGAATGCTTATGAGAATGAAAATGAGGTAATT
TCAACAGATGAAAGTGAGAACTCCTCCAAGTCTCCTGGAAATAAACCAAACAACATAAAGTCAAAAGCTACTCCATGGAC
CTCTTTTCTGCCTCCGTCAGTCCCTATGCCAGGATCAGGACTGGGACCAGCAAAGTCAGGCCTAAACTTCAATGCCCCCC
CCCACTCCCCT

Alignment

ORF - retro_dnov_1239 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.09 %
• Parental protein coverage: 50.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ITTPLKQWKVGDKCSAIWSEDGCIYPATIASIDFKRDTCVVVYTGYGNREEQNLSDLLFPTFEGVNNVEQ
          I.TPLKQ.KVG..CSA.WSED.C...A.IA.IDFK...C.VVYTG.GNRE.QNLSDLLFPT.EGVNNVEQ
Retrocopy IATPLKQRKVGNICSAVWSEDSCTHSAAIAFIDFKSGNCAVVYTGNGNREKQNLSDLLFPTLEGVNNVEQ

Parental  NAQENENESQLSTDESENSSKSPGNKPNNIKSKATTWNSFLPPPPPMPGSGLGPGKSGLKFNGPPPPP
          NA.ENENE...STDESENSSKSPGNKPNNIKSKAT.W.SFLPP..PMPGSGLGP.KSGL.FN.....P
Retrocopy NAYENENE-VISTDESENSSKSPGNKPNNIKSKATPWTSFLPPSVPMPGSGLGPAKSGLNFNXXXXSP

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	0.00 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	0.00 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_1239 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,