RetrogeneDB ID: retro_dnov_477

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_5149:79181..79462(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLNS1A
• Ensembl ID: ENSDNOG00000008188
• Aliases: None
• Description: chloride channel, nucleotide-sensitive, 1A [Source:HGNC Symbol;Acc:2080]

Sequence

>retro_dnov_477
GAATCTGTTGCTGATGAAAAAGAGGGAGACTGTGATGATGATGATGAACCTATTGCTGAGTTTAGATTTGTACCTAGTGA
TAAATCAGCATTGGAAGGAATATTTGCCGCAATGTGTGAATGCCAGGCTTTGCCTCCAGATCGTGAGGATGAAGGTTCAT
GTGATTATGATGGGGAAGAGTATGATGTGGAAGCAAATGAACAAGGGCAGGGGGACATCCCTACTTTTACACCAATGAAG
GACTGTTCGATTTAACAGCAGAAGGCCAAGCCACATCCGAG

Alignment

ORF - retro_dnov_477 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.25 %
• Parental protein coverage: 54.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ESVADEEDEDKDDDDEPIAEFRFVPSDKSALEAMFTAMCECQALHPDPEDEDSDDYDGEEYDVEAHEQGQ
          ESVADE...D.DDDDEPIAEFRFVPSDKSALE..F.AMCECQAL.PD.EDE.S.DYDGEEYDVEA.EQGQ
Retrocopy ESVADEKEGDCDDDDEPIAEFRFVPSDKSALEGIFAAMCECQALPPDREDEGSCDYDGEEYDVEANEQGQ

Parental  GDIPT-FYTYEEGLSHLTAEGQATLE
          GDIPT.FYT..EGL..LTAEGQAT.E
Retrocopy GDIPT<FYT-NEGLFDLTAEGQATSE

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	13.03 RPM
SRP012922_cerebellum	0.00 RPM	10.45 RPM
SRP012922_heart	0.00 RPM	6.26 RPM
SRP012922_kidney	0.00 RPM	7.94 RPM
SRP012922_liver	0.00 RPM	4.80 RPM
SRP012922_lung	0.15 RPM	11.45 RPM
SRP012922_quadricep_muscle	0.00 RPM	6.40 RPM
SRP012922_spleen	0.00 RPM	14.42 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_477 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 11 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004900	6 retrocopies	retro_cfam_1112, retro_cfam_1448, retro_cfam_255, retro_cfam_327, retro_cfam_720, retro_cfam_727,
Choloepus hoffmanni	ENSCHOG00000007254	1 retrocopy	retro_chof_1685,
Callithrix jacchus	ENSCJAG00000014927	1 retrocopy	retro_cjac_4085,
Cavia porcellus	ENSCPOG00000005260	1 retrocopy	retro_cpor_67,
Dasypus novemcinctus	ENSDNOG00000008188	1 retrocopy	retro_dnov_477 ,
Felis catus	ENSFCAG00000026321	1 retrocopy	retro_fcat_736,
Macropus eugenii	ENSMEUG00000005935	4 retrocopies	retro_meug_1825, retro_meug_2097, retro_meug_783, retro_meug_929,
Myotis lucifugus	ENSMLUG00000024623	2 retrocopies	retro_mluc_1501, retro_mluc_1507,
Mustela putorius furo	ENSMPUG00000015944	1 retrocopy	retro_mputfur_435,
Oryctolagus cuniculus	ENSOCUG00000024393	1 retrocopy	retro_ocun_1303,
Tupaia belangeri	ENSTBEG00000001316	1 retrocopy	retro_tbel_2975,