RetrogeneDB ID: retro_dnov_664

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_7412:76295..76508(-)
• Located in intron of: ENSDNOG00000010588

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM6
• Ensembl ID: ENSDNOG00000009322
• Aliases: None
• Description: LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:HGNC Symbol;Acc:17017]

Sequence

>retro_dnov_664
AGTGACTTCTTAAAGCAAATCTTAGGATGGCCAGCTGTGGTAAAATTAAATTCTAGAGTGGATTATAGAGGGGTCCTGGC
TTGCCTGGATGGTTACATGAATATAGGCCTAGAGAAGCTAGAATATGTAAATGGACAGCTGCAAAGTAAGTATGGGGATG
CAGATATCTGAGGAAACACTGTGCTACACCTAAGTACACAGAAGAGAAGGATG

Alignment

ORF - retro_dnov_664 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.39 %
• Parental protein coverage: 90. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRGNNVLYISTPKR
          SDFLKQI.G.P.VVKLNS.VDYRGVLACLDGYMNI.LE...EYVNGQL..KYGDA.I.GN.VL..ST.KR
Retrocopy SDFLKQILGWPAVVKLNSRVDYRGVLACLDGYMNIGLEKL-EYVNGQLQSKYGDADI*GNTVLHLSTQKR

Parental  GM
          .M
Retrocopy RM

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	0.19 RPM	10.31 RPM
SRP012922_cerebellum	0.00 RPM	9.90 RPM
SRP012922_heart	0.23 RPM	6.50 RPM
SRP012922_kidney	0.00 RPM	5.20 RPM
SRP012922_liver	0.00 RPM	3.10 RPM
SRP012922_lung	0.15 RPM	7.33 RPM
SRP012922_quadricep_muscle	0.00 RPM	6.75 RPM
SRP012922_spleen	0.00 RPM	9.96 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_664 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 17 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014060	1 retrocopy	retro_btau_861,
Callithrix jacchus	ENSCJAG00000002482	4 retrocopies	retro_cjac_1173, retro_cjac_1278, retro_cjac_3176, retro_cjac_3248,
Cavia porcellus	ENSCPOG00000015389	1 retrocopy	retro_cpor_368,
Dasypus novemcinctus	ENSDNOG00000009322	5 retrocopies	retro_dnov_1118, retro_dnov_176, retro_dnov_2092, retro_dnov_301, retro_dnov_664 ,
Homo sapiens	ENSG00000164167	2 retrocopies	retro_hsap_1948, retro_hsap_2107,
Gorilla gorilla	ENSGGOG00000001310	2 retrocopies	retro_ggor_1417, retro_ggor_1638,
Microcebus murinus	ENSMICG00000000571	1 retrocopy	retro_mmur_1563,
Myotis lucifugus	ENSMLUG00000026355	1 retrocopy	retro_mluc_1859,
Macaca mulatta	ENSMMUG00000005524	2 retrocopies	retro_mmul_668, retro_mmul_991,
Monodelphis domestica	ENSMODG00000000526	4 retrocopies	retro_mdom_1027, retro_mdom_1383, retro_mdom_1983, retro_mdom_621,
Mus musculus	ENSMUSG00000031683	2 retrocopies	retro_mmus_820, retro_mmus_956,
Nomascus leucogenys	ENSNLEG00000005584	2 retrocopies	retro_nleu_1275, retro_nleu_1479,
Otolemur garnettii	ENSOGAG00000026665	1 retrocopy	retro_ogar_233,
Pongo abelii	ENSPPYG00000015105	1 retrocopy	retro_pabe_1994,
Pan troglodytes	ENSPTRG00000016488	1 retrocopy	retro_ptro_1545,
Sus scrofa	ENSSSCG00000009036	2 retrocopies	retro_sscr_474, retro_sscr_475,
Tarsius syrichta	ENSTSYG00000012759	4 retrocopies	retro_tsyr_1332, retro_tsyr_1727, retro_tsyr_340, retro_tsyr_653,