RetrogeneDB ID: retro_dnov_998

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_13238:86140..86497(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED21
• Ensembl ID: ENSDNOG00000010041
• Aliases: None
• Description: mediator complex subunit 21 [Source:HGNC Symbol;Acc:11473]

Sequence

>retro_dnov_998
GCAGATGGAGTGTTGCAGCAGTGTGGTCCTCCTGCCTCTTTTAGTAATATTCAGACAGCAATTAACAAAGATCAGCCAGG
AAATCCTACAGAAGAGTATGCCCAGCTTTTTGCAGCACAAATTGCACAAACAGCAAAAGATTTTGATGTTTTGATAGATT
CCTTATCCAGTGAAGAATCTACAGCTGCATTACAGGCTGCTAGCTTGTATAAACTTGAAGAAGAAAACCATGAAACTGCT
ACATGTCTGGAGGATGTTGTTTATCGAGGAGATATGCTTCTGGAAAAGATACAAAGAGCACTTGCTGATATTGAGCAATC
ATAGTTGAAAACAAGAAGTAGTACCCATAGCCAATCT

Alignment

ORF - retro_dnov_998 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.47 %
• Parental protein coverage: 82.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AIGVLQQCGPPASFSNIQTAINKDQPANPTEEYAQLFAALIARTAKXXXXXXXXXXXXXXXXXXXAASLY
          A.GVLQQCGPPASFSNIQTAINKDQP.NPTEEYAQLFAA.IA.TAK...................AASLY
Retrocopy ADGVLQQCGPPASFSNIQTAINKDQPGNPTEEYAQLFAAQIAQTAKDFDVLIDSLSSEESTAALQAASLY

Parental  KLEEENHEAATCLEDVVYRGDMLLEKIQSALADIAQSQLKTRSGTHSQS
          KLEEENHE.ATCLEDVVYRGDMLLEKIQ.ALADI.QS.LKTRS.THSQS
Retrocopy KLEEENHETATCLEDVVYRGDMLLEKIQRALADIEQS*LKTRSSTHSQS

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	1.36 RPM	12.83 RPM
SRP012922_cerebellum	2.61 RPM	18.97 RPM
SRP012922_heart	1.62 RPM	23.90 RPM
SRP012922_kidney	1.64 RPM	13.69 RPM
SRP012922_liver	1.86 RPM	9.13 RPM
SRP012922_lung	2.29 RPM	16.34 RPM
SRP012922_quadricep_muscle	3.29 RPM	25.27 RPM
SRP012922_spleen	3.66 RPM	24.15 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_998 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011670	1 retrocopy	retro_amel_108,
Dasypus novemcinctus	ENSDNOG00000010041	1 retrocopy	retro_dnov_998 ,
Echinops telfairi	ENSETEG00000006223	1 retrocopy	retro_etel_1141,
Felis catus	ENSFCAG00000030691	1 retrocopy	retro_fcat_1101,
Homo sapiens	ENSG00000152944	1 retrocopy	retro_hsap_4105,
Gorilla gorilla	ENSGGOG00000016313	1 retrocopy	retro_ggor_2756,
Myotis lucifugus	ENSMLUG00000007678	1 retrocopy	retro_mluc_229,
Macaca mulatta	ENSMMUG00000003218	1 retrocopy	retro_mmul_2365,
Nomascus leucogenys	ENSNLEG00000005431	1 retrocopy	retro_nleu_573,
Pongo abelii	ENSPPYG00000004377	1 retrocopy	retro_pabe_3361,
Pan troglodytes	ENSPTRG00000004785	1 retrocopy	retro_ptro_2786,
Pteropus vampyrus	ENSPVAG00000013357	1 retrocopy	retro_pvam_449,
Ictidomys tridecemlineatus	ENSSTOG00000008391	2 retrocopies	retro_itri_1005, retro_itri_1057,