RetrogeneDB ID: retro_dnov_1002

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_132990:1326..1635(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000015116
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000018952
• Aliases: None
• Description: None

Sequence

>retro_dnov_1002
GGGACTTTTAAACTTGAACTATTCCTTCCAGAACAATATCCAATGGCAGTCCCTAAAGTACATTTCATGACCAAAATTTA
TCACCCTAATGTAAACAAGTTGGGAAGAATATGTTTAGATATTTTGAGAGATAAATGGCCGCCAGCACTGCAGATCTGCA
CAGTTTTGCTATCCATACAGGCTTTGTTAAATGCTCCCGGTACAGATGATCCATTAGCAAATTATGTAGCAGAGCAGTGG
AAGTCCAAGGAAGCCCAAAACATAGAAACAACTAGAGCATGGGTTAGACTATATGCCATAAGTAATATT

Alignment

ORF - retro_dnov_1002 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.55 %
• Parental protein coverage: 67.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDD
          GTFKLELFLPE.YPMA.PKV.FMTKIYHPNV.KLGRICLDIL.DKW.PALQI.TVLLSIQALL.AP..DD
Retrocopy GTFKLELFLPEQYPMAVPKVHFMTKIYHPNVNKLGRICLDILRDKWPPALQICTVLLSIQALLNAPGTDD

Parental  PLANDVAEQWKTNEAQAIETARAWSRPYAMNNI
          PLAN.VAEQWK..EAQ.IET.RAW.R.YA..NI
Retrocopy PLANYVAEQWKSKEAQNIETTRAWVRLYAISNI

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	31.70 RPM
SRP012922_cerebellum	0.00 RPM	50.73 RPM
SRP012922_heart	0.00 RPM	23.20 RPM
SRP012922_kidney	0.00 RPM	24.92 RPM
SRP012922_liver	0.00 RPM	15.79 RPM
SRP012922_lung	0.00 RPM	25.81 RPM
SRP012922_quadricep_muscle	0.00 RPM	26.48 RPM
SRP012922_spleen	0.00 RPM	30.33 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_1002 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 16 parental genes, and 62 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006177	1 retrocopy	retro_cfam_196,
Callithrix jacchus	ENSCJAG00000002979	8 retrocopies	retro_cjac_141, retro_cjac_2121, retro_cjac_3142, retro_cjac_3148, retro_cjac_3216, retro_cjac_3241, retro_cjac_3329, retro_cjac_425,
Cavia porcellus	ENSCPOG00000008581	5 retrocopies	retro_cpor_1548, retro_cpor_230, retro_cpor_24, retro_cpor_655, retro_cpor_750,
Dasypus novemcinctus	ENSDNOG00000018952	9 retrocopies	retro_dnov_1002 , retro_dnov_1066, retro_dnov_1107, retro_dnov_1185, retro_dnov_1487, retro_dnov_1977, retro_dnov_2598, retro_dnov_277, retro_dnov_492,
Echinops telfairi	ENSETEG00000001882	5 retrocopies	retro_etel_1008, retro_etel_1417, retro_etel_1593, retro_etel_1661, retro_etel_2136,
Homo sapiens	ENSG00000177889	3 retrocopies	retro_hsap_1392, retro_hsap_17, retro_hsap_3124,
Loxodonta africana	ENSLAFG00000028985	1 retrocopy	retro_lafr_57,
Macropus eugenii	ENSMEUG00000002944	7 retrocopies	retro_meug_1236, retro_meug_1287, retro_meug_1453, retro_meug_1473, retro_meug_162, retro_meug_2009, retro_meug_31,
Microcebus murinus	ENSMICG00000014081	4 retrocopies	retro_mmur_1351, retro_mmur_220, retro_mmur_267, retro_mmur_611,
Macaca mulatta	ENSMMUG00000020634	3 retrocopies	retro_mmul_1587, retro_mmul_234, retro_mmul_72,
Monodelphis domestica	ENSMODG00000009451	2 retrocopies	retro_mdom_133, retro_mdom_1485,
Oryctolagus cuniculus	ENSOCUG00000011287	1 retrocopy	retro_ocun_100,
Pongo abelii	ENSPPYG00000004832	4 retrocopies	retro_pabe_113, retro_pabe_1152, retro_pabe_2580, retro_pabe_3326,
Pan troglodytes	ENSPTRG00000005297	3 retrocopies	retro_ptro_2112, retro_ptro_3253, retro_ptro_956,
Sarcophilus harrisii	ENSSHAG00000007776	1 retrocopy	retro_shar_105,
Tarsius syrichta	ENSTSYG00000008800	5 retrocopies	retro_tsyr_1476, retro_tsyr_1754, retro_tsyr_207, retro_tsyr_348, retro_tsyr_5,