RetrogeneDB ID: retro_dnov_588

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_6557:4022..4458(+)
• Located in intron of: ENSDNOG00000024009

Retrocopy information

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

Parental gene information

• Parental gene symbol: AK2
• Ensembl ID: ENSDNOG00000014113
• Aliases: None
• Description: adenylate kinase 2 [Source:HGNC Symbol;Acc:362]

Sequence

>retro_dnov_588
AATCGTTTTCTTCTAGATGACTTCCCTTGGACTGTGAGGCAGGCAGAAATGCTCAACAACCTCATGGAGAAGAGGTAAGA
GAAGCTTAATTCTGTAATTGAATTCAGGATTCCAGACTCTCTGCTTATCTGGAGAATCACAGGAAGACTGATTCACCCCA
CAAGTAGCTGTACCTACCATAAGGAATTCAGCCTGCCTAAGAAGCCTATGAAAGATGATATCACCGGGGAACCTTTGGTC
CACTGATCAGATGATAATGAGAAGGCCTTGAAAATCCACCTGGATTCATACCACACTCAGACCACCCCACTGGTGGAATA
CACAGTAAGCTGGAATCCACTCTGCCATCGATGTAACGCAGACCCCTGACGTCGTGTTTGCAAGCATCTTAGCAGCCTTC
TCCAAAGCCACATGTAAAGACTTGGTTATGTTTATC

Alignment

ORF - retro_dnov_588 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.49 %
• Parental protein coverage: 60.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NGFLLDGFPRTVRQAEMLDDLMEKRKEKLNSVIEFSIPDSLLIRRITGRLIHPTSGRTYHKEFSPPKEPM
          N.FLLD.FP.TVRQAEML..LMEKR.EKLNSVIEF.IPDSLLI.RITGRLIHPTS..TYHKEFS.PK.PM
Retrocopy NRFLLDDFPWTVRQAEMLNNLMEKR*EKLNSVIEFRIPDSLLIWRITGRLIHPTSSCTYHKEFSLPKKPM

Parental  KDDITGEPLVHRSDDNEKALKIRLDSYHTQTIPLVEY-YSK-RGIHSAIDATQTPDVVFASILAAFSKAT
          KDDITGEPLVH.SDDNEKALKI.LDSYHTQT.PLVEY..SK..GIHSAID.TQTPDVVFASILAAFSKAT
Retrocopy KDDITGEPLVH*SDDNEKALKIHLDSYHTQTTPLVEY<HSK<AGIHSAIDVTQTPDVVFASILAAFSKAT

Parental  CKDLVMFI
          CKDLVMFI
Retrocopy CKDLVMFI

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	0.58 RPM	73.31 RPM
SRP012922_cerebellum	0.00 RPM	16.77 RPM
SRP012922_heart	0.23 RPM	23.20 RPM
SRP012922_kidney	0.00 RPM	20.53 RPM
SRP012922_liver	0.31 RPM	146.76 RPM
SRP012922_lung	0.00 RPM	13.90 RPM
SRP012922_quadricep_muscle	0.00 RPM	16.10 RPM
SRP012922_spleen	0.00 RPM	23.01 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_588 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 21 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017605	2 retrocopies	retro_btau_1146, retro_btau_1168,
Canis familiaris	ENSCAFG00000010390	1 retrocopy	retro_cfam_1622,
Callithrix jacchus	ENSCJAG00000001105	1 retrocopy	retro_cjac_509,
Dasypus novemcinctus	ENSDNOG00000014113	4 retrocopies	retro_dnov_1077, retro_dnov_2052, retro_dnov_2690, retro_dnov_588 ,
Echinops telfairi	ENSETEG00000002333	2 retrocopies	retro_etel_1466, retro_etel_309,
Homo sapiens	ENSG00000004455	1 retrocopy	retro_hsap_395,
Gorilla gorilla	ENSGGOG00000000069	1 retrocopy	retro_ggor_395,
Myotis lucifugus	ENSMLUG00000000793	1 retrocopy	retro_mluc_1463,
Macaca mulatta	ENSMMUG00000006284	1 retrocopy	retro_mmul_1326,
Monodelphis domestica	ENSMODG00000017363	1 retrocopy	retro_mdom_1792,
Nomascus leucogenys	ENSNLEG00000003152	1 retrocopy	retro_nleu_1313,
Oryctolagus cuniculus	ENSOCUG00000001832	2 retrocopies	retro_ocun_1280, retro_ocun_445,
Otolemur garnettii	ENSOGAG00000000818	1 retrocopy	retro_ogar_2760,
Ochotona princeps	ENSOPRG00000005023	1 retrocopy	retro_opri_822,
Pongo abelii	ENSPPYG00000001579	1 retrocopy	retro_pabe_1965,
Pan troglodytes	ENSPTRG00000000499	1 retrocopy	retro_ptro_1587,
Rattus norvegicus	ENSRNOG00000000122	3 retrocopies	retro_rnor_1965, retro_rnor_2315, retro_rnor_974,
Sorex araneus	ENSSARG00000000202	1 retrocopy	retro_sara_556,
Sus scrofa	ENSSSCG00000024355	1 retrocopy	retro_sscr_714,
Ictidomys tridecemlineatus	ENSSTOG00000016042	1 retrocopy	retro_itri_595,
Tursiops truncatus	ENSTTRG00000008979	2 retrocopies	retro_ttru_1579, retro_ttru_978,