RetrogeneDB ID: retro_dnov_8

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_83982:4887..5259(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000018790
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000010921
• Aliases: None
• Description: None

Sequence

>retro_dnov_8
AAGTACCTGGCCCACATCATTGTAATGGGAATGCAGGTGGTGGGCAGGACCTTCACCCAGGCCCTGCGGCAGGAGTTTGC
AGCCAACCAGGCAGCAGCAGATTCCCAGGGACATGCTGGACACCAGCCTGCAGCCACATCCAACCTCCCCAGCATCAGCC
TCCAGGAGGCACAGCAGATTCTCAACATATCCAAGCTGAGAATCGAGGAGATCCACGAGAACTATCACCACTTATTTAAG
ATGAATGATAAATCTGCGGGTGGCTCCTTCTACCTGCAGTTAAAGGTGGTCCAAGCAAAGGAGCACCTTGATGAGCAACT
CAGAATCCAGGCCCACAAGGACAGGGAAAAAGGACAGACATCTAAAACATGA

Alignment

ORF - retro_dnov_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.98 %
• Parental protein coverage: 98.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KYLAQIIVMGVQVVGRAFARALRQEFAASRAAADARGRAGHQSAAASNLSGLSLQEAQQILNVSKLRPEE
          KYLA.IIVMG.QVVGR.F..ALRQEFAA..AAAD..G.AGHQ.AA.SNL...SLQEAQQILN.SKLR.EE
Retrocopy KYLAHIIVMGMQVVGRTFTQALRQEFAANQAAADSQGHAGHQPAATSNLPSISLQEAQQILNISKLRIEE

Parental  IQKNYDHLFKVNDKSVGGSFYLQSKXVRAKERLDEELRIQAQEDREEGETPKT
          I..NY.HLFK.NDKS.GGSFYLQ.K.V.AKE.LDE.LRIQA..DRE.G.T.KT
Retrocopy IHENYHHLFKMNDKSAGGSFYLQLKVVQAKEHLDEQLRIQAHKDREKGQTSKT

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	44.53 RPM
SRP012922_cerebellum	0.00 RPM	32.72 RPM
SRP012922_heart	0.00 RPM	66.36 RPM
SRP012922_kidney	0.00 RPM	27.65 RPM
SRP012922_liver	0.00 RPM	22.14 RPM
SRP012922_lung	0.00 RPM	19.55 RPM
SRP012922_quadricep_muscle	0.00 RPM	56.25 RPM
SRP012922_spleen	0.00 RPM	21.29 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_8 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 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009200	1 retrocopy	retro_btau_1664,
Canis familiaris	ENSCAFG00000019226	1 retrocopy	retro_cfam_1967,
Callithrix jacchus	ENSCJAG00000019772	1 retrocopy	retro_cjac_1148,
Dasypus novemcinctus	ENSDNOG00000010921	2 retrocopies	retro_dnov_1361, retro_dnov_8 ,
Dipodomys ordii	ENSDORG00000014888	1 retrocopy	retro_dord_81,
Equus caballus	ENSECAG00000019387	1 retrocopy	retro_ecab_302,
Erinaceus europaeus	ENSEEUG00000007432	7 retrocopies	retro_eeur_138, retro_eeur_171, retro_eeur_213, retro_eeur_234, retro_eeur_273, retro_eeur_440, retro_eeur_673,
Echinops telfairi	ENSETEG00000006416	1 retrocopy	retro_etel_2070,
Felis catus	ENSFCAG00000027971	1 retrocopy	retro_fcat_520,
Myotis lucifugus	ENSMLUG00000008921	6 retrocopies	retro_mluc_2446, retro_mluc_2447, retro_mluc_2448, retro_mluc_2516, retro_mluc_2517, retro_mluc_429,
Mus musculus	ENSMUSG00000014301	1 retrocopy	retro_mmus_73,
Rattus norvegicus	ENSRNOG00000004608	1 retrocopy	retro_rnor_713,
Sus scrofa	ENSSSCG00000007947	2 retrocopies	retro_sscr_1090, retro_sscr_468,
Ictidomys tridecemlineatus	ENSSTOG00000003461	1 retrocopy	retro_itri_1732,
Tupaia belangeri	ENSTBEG00000001347	1 retrocopy	retro_tbel_3190,
Tarsius syrichta	ENSTSYG00000009306	1 retrocopy	retro_tsyr_282,