RetrogeneDB ID: retro_dnov_373

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_4186:107391..107708(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM230
• Ensembl ID: ENSDNOG00000005724
• Aliases: None
• Description: transmembrane protein 230 [Source:HGNC Symbol;Acc:15876]

Sequence

>retro_dnov_373
CAGCTGTGTCAGCTTGTTAGGCTACCATCTCCACCAACCTGGCTACTGGAATCCCCAGGAGTAAAGTGAAATGCTCAAGG
CTCTCCAGCCCAGACGATGGCTACATTGACCTTCAGTTTAAGAAAAGCCCTCCTCGGCTCCCCTCTAAGGCCCTTGCGCT
TGCCGCCGTGCTGTTTTCAGTTGGCGCCTTGCTCGCCATGATAGGCTCCTCCTGCGGCGGGCGCCATCACAGAGAGGAGG
CAGACCTGGCCGTTCCTGTCCTGATCGCTGGCATCCAGGCATTCCTGCCCAGTTTTGGCCACCTGCACATCGCCTAC

Alignment

ORF - retro_dnov_373 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.59 %
• Parental protein coverage: 77.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RLCQLVMMPS-RTNLATGIPSSKVKYSRLSSTDDGYIDLQFKKSPPKIPYKAIALATVLFLIGAFLIIIG
          .LCQLV..PS..TNLATGIP.SKVK.SRLSS.DDGYIDLQFKKSPP..P.KA.ALA.VLF..GA.L..IG
Retrocopy QLCQLVRLPS<STNLATGIPRSKVKCSRLSSPDDGYIDLQFKKSPPRLPSKALALAAVLFSVGALLAMIG

Parental  SLLLAGYISKGGADRAVPVLIIGILVFLPGFYHLRIAY
          S....G......AD.AVPVLI.GI..FLP.F.HL.IAY
Retrocopy S-SCGGRHHREEADLAVPVLIAGIQAFLPSFGHLHIAY

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	20.03 RPM
SRP012922_cerebellum	0.27 RPM	12.23 RPM
SRP012922_heart	0.00 RPM	3.94 RPM
SRP012922_kidney	0.00 RPM	19.44 RPM
SRP012922_liver	0.00 RPM	9.91 RPM
SRP012922_lung	0.00 RPM	22.60 RPM
SRP012922_quadricep_muscle	0.00 RPM	5.19 RPM
SRP012922_spleen	0.00 RPM	22.78 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_373 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 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009083	1 retrocopy	retro_amel_1818,
Bos taurus	ENSBTAG00000006063	2 retrocopies	retro_btau_1079, retro_btau_147,
Canis familiaris	ENSCAFG00000006039	1 retrocopy	retro_cfam_981,
Dasypus novemcinctus	ENSDNOG00000005724	5 retrocopies	retro_dnov_1004, retro_dnov_2377, retro_dnov_2534, retro_dnov_373 , retro_dnov_803,
Myotis lucifugus	ENSMLUG00000023089	2 retrocopies	retro_mluc_1504, retro_mluc_1759,
Ochotona princeps	ENSOPRG00000008611	1 retrocopy	retro_opri_502,
Pteropus vampyrus	ENSPVAG00000002863	1 retrocopy	retro_pvam_44,
Ictidomys tridecemlineatus	ENSSTOG00000019378	1 retrocopy	retro_itri_35,