RetrogeneDB ID: retro_dnov_1004

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_13353:191..560(+)
• 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_1004
TGTCAGCTTGTTATGACACCATCTGGTACCAATCTGGCTACGGGAATCTCCAGTAATAAATTGAAATACTCCAGTCTCGA
CAGCACAGATGATGTCTACCTTGACCTTCAGTTTAAGAAAAGCCCTCCCAAAAATTCTTATAAAGCCATTGCACTTGCCA
CCATGCTATTTTTGATTGGCACCTTTCTCTCTCTCCCTCTTGCTGGCAGCCTACAAGAGCAAAGGAGAGTAGGGGCAGAA
TGGACCATTCCTATCCTGATCATTGGCATTCTGGTGTTCCTGCCAGGTTTGTACCATCTGCACATTGTCTACTATGTACC
CAAAGGCTACCGGGGTTACTCCTACAATGACATTCCTGACTTTGATGAT

Alignment

ORF - retro_dnov_1004 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.08 %
• Parental protein coverage: 89.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CQLVMMPSRTNLATGIPSSKVKYSRLSSTDDGYIDLQFKKSPPKIPYKAIALATVLFLIGAFLIIIGSLL
          CQLVM.PS.TNLATGI.S.K.KYS.L.STDD.Y.DLQFKKSPPK..YKAIALAT.LFLIG.FL....SL.
Retrocopy CQLVMTPSGTNLATGISSNKLKYSSLDSTDDVYLDLQFKKSPPKNSYKAIALATMLFLIGTFL----SLP

Parental  LAGYIS---KGGADRAVPVLIIGILVFLPGFYHLRIAYYASQGYRGYSYDDIPDFDD
          LAG........GA....P.LIIGILVFLPG.YHL.I.YY...GYRGYSY.DIPDFDD
Retrocopy LAGSLQEQRRVGAEWTIPILIIGILVFLPGLYHLHIVYYVPKGYRGYSYNDIPDFDD

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	0.00 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_1004 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,