RetrogeneDB ID: retro_dnov_201

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_256:8835..9207(+)
• Located in intron of: ENSDNOG00000003528

Retrocopy information

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

Parental gene information

• Parental gene symbol: HINT2
• Ensembl ID: ENSDNOG00000009083
• Aliases: None
• Description: histidine triad nucleotide binding protein 2 [Source:HGNC Symbol;Acc:18344]

Sequence

>retro_dnov_201
GATGAGATCGCCAAGGCTCAGGCCACTCCACCTGGTGGTGACACGATCTTCGGGAAGATTATCCACAAGGAAATCCCCAC
CAAAATCATTTTTGAAGATGACCAGAGTCTTGCTTTCCATAACATATCCCCACAAGCATCAACACATTTTCTGGTGATTC
CTAAAAAACATATTTCTCAGATTTCTGTAGCATAAGATGATGATGAAAGGCAACTTGGACATTTAATGATTGTTGGCAAG
AAATGTGCTGCTGATCTGGGCCTAAAGAAGGGTTATGGAATGGTGGTGAATGAAGGTTCAGAGGGAGGGCAGTCTGTCTG
TCCCGTTCATCTCCATGTTCTTGGAGGTCGGCAGATGAGTTGGCCTCCTGGG

Alignment

ORF - retro_dnov_201 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.38 %
• Parental protein coverage: 92.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NEVAKAQQAAPGAAAPTIFSRILDRSLPADILYEDQQCLVFRDVAPQAPVHFLVIPKKPIPRISQAEEED
          .E.AKAQ...PG....TIF..I.....P..I..ED.Q.L.F....PQA..HFLVIPKK.I..IS.A...D
Retrocopy DEIAKAQATPPGG--DTIFGKIIHKEIPTKIIFEDDQSLAFHNISPQASTHFLVIPKKHISQISVA*DDD

Parental  EQLLGHLLLVAKKAAKAEGLGDGYRLVINDGKLGAQSVYHLHIHVLGGRQLQWPPG
          E..LGHL..V.KK.A...GL..GY..V.N.G..G.QSV...H.HVLGGRQ..WPPG
Retrocopy ERQLGHLMIVGKKCAADLGLKKGYGMVVNEGSEGGQSVCPVHLHVLGGRQMSWPPG

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	3.89 RPM	29.75 RPM
SRP012922_cerebellum	2.61 RPM	21.58 RPM
SRP012922_heart	2.32 RPM	30.63 RPM
SRP012922_kidney	16.98 RPM	134.71 RPM
SRP012922_liver	11.46 RPM	74.93 RPM
SRP012922_lung	4.12 RPM	50.09 RPM
SRP012922_quadricep_muscle	2.77 RPM	11.60 RPM
SRP012922_spleen	4.58 RPM	33.31 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_201 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 18 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011444	1 retrocopy	retro_btau_1129,
Callithrix jacchus	ENSCJAG00000010068	1 retrocopy	retro_cjac_1343,
Cavia porcellus	ENSCPOG00000000419	1 retrocopy	retro_cpor_181,
Dasypus novemcinctus	ENSDNOG00000009083	2 retrocopies	retro_dnov_201 , retro_dnov_854,
Echinops telfairi	ENSETEG00000017929	1 retrocopy	retro_etel_486,
Homo sapiens	ENSG00000137133	1 retrocopy	retro_hsap_2603,
Gorilla gorilla	ENSGGOG00000011265	1 retrocopy	retro_ggor_1823,
Loxodonta africana	ENSLAFG00000015022	1 retrocopy	retro_lafr_737,
Macaca mulatta	ENSMMUG00000016337	1 retrocopy	retro_mmul_1509,
Nomascus leucogenys	ENSNLEG00000026914	1 retrocopy	retro_nleu_1534,
Oryctolagus cuniculus	ENSOCUG00000027206	1 retrocopy	retro_ocun_66,
Otolemur garnettii	ENSOGAG00000011830	1 retrocopy	retro_ogar_765,
Pongo abelii	ENSPPYG00000019082	1 retrocopy	retro_pabe_2310,
Pan troglodytes	ENSPTRG00000020923	1 retrocopy	retro_ptro_1754,
Pteropus vampyrus	ENSPVAG00000003028	1 retrocopy	retro_pvam_842,
Tupaia belangeri	ENSTBEG00000013020	1 retrocopy	retro_tbel_4676,
Tarsius syrichta	ENSTSYG00000002700	7 retrocopies	retro_tsyr_1210, retro_tsyr_1356, retro_tsyr_1483, retro_tsyr_1485, retro_tsyr_311, retro_tsyr_468, retro_tsyr_48,
Tursiops truncatus	ENSTTRG00000011932	1 retrocopy	retro_ttru_1302,