RetrogeneDB ID: retro_dnov_1836

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_32746:31704..31974(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM5
• Ensembl ID: ENSDNOG00000008121
• Aliases: None
• Description: LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:HGNC Symbol;Acc:17162]

Sequence

>retro_dnov_1836
ATGGCTGCTAATGCGACTACTAACCCGTCGCAGCTACTGCCACTAGAGTTTGTAGGTAAGTGTATAGGATCAAGAATTCA
TGTTGTAATGAAGAGTGATAAAGAAATTGTTGGTACACTTCTAGGATTCAACAACTTTGTCAATATGGTACTGGAAGACA
TCACCGAGTTTGAAATCATCCCAGAAAGAAGGATTACTAAATTAGATAAAATTTTGCTAAATGGAAATAATATAACAATG
CTGGTTCCTGGAGGAGAAAGACCTGAAGTA

Alignment

ORF - retro_dnov_1836 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.81 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAANATTNPSQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEITPEGRRITKLD
          MAANATTNPSQLLPLE.V.KCIGSRIH.VMKSDKEIVGTLLGF..FVNMVLED.TEFEI.PE.RRITKLD
Retrocopy MAANATTNPSQLLPLEFVGKCIGSRIHVVMKSDKEIVGTLLGFNNFVNMVLEDITEFEIIPE-RRITKLD

Parental  E-MLNGNNITMLVPGGEGPEV
          ...LNGNNITMLVPGGE.PEV
Retrocopy KILLNGNNITMLVPGGERPEV

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	7.58 RPM
SRP012922_cerebellum	0.00 RPM	5.09 RPM
SRP012922_heart	0.00 RPM	6.26 RPM
SRP012922_kidney	0.00 RPM	3.83 RPM
SRP012922_liver	0.00 RPM	2.94 RPM
SRP012922_lung	0.00 RPM	9.16 RPM
SRP012922_quadricep_muscle	0.00 RPM	2.77 RPM
SRP012922_spleen	0.00 RPM	11.45 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_1836 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 6 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009185	3 retrocopies	retro_cjac_1883, retro_cjac_2760, retro_cjac_3068,
Dasypus novemcinctus	ENSDNOG00000008121	1 retrocopy	retro_dnov_1836 ,
Pongo abelii	ENSPPYG00000017661	1 retrocopy	retro_pabe_3449,
Rattus norvegicus	ENSRNOG00000042126	3 retrocopies	retro_rnor_1171, retro_rnor_567, retro_rnor_694,
Ictidomys tridecemlineatus	ENSSTOG00000012662	4 retrocopies	retro_itri_1199, retro_itri_188, retro_itri_222, retro_itri_415,
Tarsius syrichta	ENSTSYG00000006449	9 retrocopies	retro_tsyr_1022, retro_tsyr_1080, retro_tsyr_1579, retro_tsyr_181, retro_tsyr_1837, retro_tsyr_1863, retro_tsyr_1963, retro_tsyr_577, retro_tsyr_96,