RetrogeneDB ID: retro_dnov_2000

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_41455:1126..1413(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000024253
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CDK2AP1
• Ensembl ID: ENSDNOG00000017145
• Aliases: None
• Description: cyclin-dependent kinase 2 associated protein 1 [Source:HGNC Symbol;Acc:14002]

Sequence

>retro_dnov_2000
GGAAGTGTCCACTCTCCTTCTACCAGTATGGCGACATCCTTGCAGTACCACCAGCTGCTGAGTGACTATGGCAGCCATCC
CTTGGCTACACCCAGGGAACTGGGAAGAGCCAGGTGCCCCAAAGCAAATATGCTGAGCTGCTGGCCATCATCAAAGAGCT
GGGGAAAGAGATCAGACCCACCTACGCAGGGAGCAAGAGCGCCATGAAGAGATTGAAACGAGGCATCATTCATGCTAGAG
GACTGGTTCGGGAGTGCTTGGCCAAAACAGAAAAGAATGCCAGATCC

Alignment

ORF - retro_dnov_2000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GSVHSPSTSMATSSQYRQLLSDYGP-PSLGYTQGTGNSQVPQSKYAELLAIIEELGKEIRPTYAGSKSAM
          GSVHSPSTSMATS.QY.QLLSDYG..PSLGYTQGTG.SQVPQSKYAELLAII.ELGKEIRPTYAGSKSAM
Retrocopy GSVHSPSTSMATSLQYHQLLSDYGS<PSLGYTQGTGKSQVPQSKYAELLAIIKELGKEIRPTYAGSKSAM

Parental  ERLKRGIIHARGLVRECLAETERNARS
          .RLKRGIIHARGLVRECLA.TE.NARS
Retrocopy KRLKRGIIHARGLVRECLAKTEKNARS

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	4.86 RPM
SRP012922_cerebellum	0.00 RPM	9.90 RPM
SRP012922_heart	0.00 RPM	5.57 RPM
SRP012922_kidney	0.00 RPM	4.65 RPM
SRP012922_liver	0.00 RPM	1.24 RPM
SRP012922_lung	0.00 RPM	8.25 RPM
SRP012922_quadricep_muscle	0.00 RPM	2.94 RPM
SRP012922_spleen	0.00 RPM	12.93 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_2000 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 19 parental genes, and 60 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015147	1 retrocopy	retro_amel_19,
Choloepus hoffmanni	ENSCHOG00000010939	1 retrocopy	retro_chof_56,
Dasypus novemcinctus	ENSDNOG00000017145	21 retrocopies	retro_dnov_1094, retro_dnov_1097, retro_dnov_1236, retro_dnov_1502, retro_dnov_1569, retro_dnov_1656, retro_dnov_1750, retro_dnov_1979, retro_dnov_2000 , retro_dnov_2145, retro_dnov_2249, retro_dnov_2527, retro_dnov_2661, retro_dnov_2662, retro_dnov_2673, retro_dnov_270, retro_dnov_687, retro_dnov_69, retro_dnov_70, retro_dnov_729, retro_dnov_741,
Felis catus	ENSFCAG00000026822	1 retrocopy	retro_fcat_1578,
Homo sapiens	ENSG00000111328	2 retrocopies	retro_hsap_2227, retro_hsap_2834,
Gorilla gorilla	ENSGGOG00000009567	1 retrocopy	retro_ggor_1968,
Macropus eugenii	ENSMEUG00000009438	12 retrocopies	retro_meug_1101, retro_meug_1112, retro_meug_1218, retro_meug_1366, retro_meug_1509, retro_meug_1565, retro_meug_2116, retro_meug_377, retro_meug_404, retro_meug_669, retro_meug_836, retro_meug_868,
Monodelphis domestica	ENSMODG00000012451	2 retrocopies	retro_mdom_1845, retro_mdom_611,
Mustela putorius furo	ENSMPUG00000001667	1 retrocopy	retro_mputfur_1601,
Mus musculus	ENSMUSG00000029394	1 retrocopy	retro_mmus_125,
Nomascus leucogenys	ENSNLEG00000001478	2 retrocopies	retro_nleu_1209, retro_nleu_2686,
Otolemur garnettii	ENSOGAG00000024823	1 retrocopy	retro_ogar_2292,
Pongo abelii	ENSPPYG00000005083	2 retrocopies	retro_pabe_1974, retro_pabe_2198,
Pan troglodytes	ENSPTRG00000005596	3 retrocopies	retro_ptro_1574, retro_ptro_1921, retro_ptro_2929,
Pteropus vampyrus	ENSPVAG00000015302	1 retrocopy	retro_pvam_478,
Rattus norvegicus	ENSRNOG00000001070	3 retrocopies	retro_rnor_1717, retro_rnor_1718, retro_rnor_1753,
Sarcophilus harrisii	ENSSHAG00000015009	1 retrocopy	retro_shar_366,
Sus scrofa	ENSSSCG00000009775	2 retrocopies	retro_sscr_992, retro_sscr_993,
Tursiops truncatus	ENSTTRG00000015881	2 retrocopies	retro_ttru_312, retro_ttru_464,