RetrogeneDB ID: retro_dnov_2238

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_57899:5723..6051(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAX1BP3
• Ensembl ID: ENSDNOG00000023829
• Aliases: None
• Description: Tax1 (human T-cell leukemia virus type I) binding protein 3 [Source:HGNC Symbol;Acc:30684]

Sequence

>retro_dnov_2238
CAAAGAGTTGAAATTCATATGCTGCGCCCAGGTGAGAACTTAATCCTGGGCTTCTGCCTTGAGGAGATATTGACCAGGAC
CCCTCCCAGAACCCCTTCCCAGAAGATAAGATGGACAAGGGCATTTATTTCACACAGTGTCTGAGGGAGGCCCTGCAGAA
ATTGCTGGGTTGCAGAGTGGAGACAAGATCATGCAGGTGAACGGCTAGGATGTGACCGTGTTCCCACACCACCAGGCTTG
GAAGCAGCTCACCAAGTGCTCCGAGGAGGTGGTGCGCCTCCTGGTGACGCGACAGTCACTGCAGAGGGCAGGGCAGCAGT
CGATGGTG

Alignment

ORF - retro_dnov_2238 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.68 %
• Parental protein coverage: 99.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QRVEIHKLRQGENLILGFSIG-GGIDQDPSQNPFSEDKTDKGIYVTR-VSEGGPAEIAGLQIGDKIMQVN
          QRVEIH.LR.GENLILGF....G.IDQDPSQNPF.EDK.DKGIY.T..VSEGGPAEIAGLQ.GDKIMQVN
Retrocopy QRVEIHMLRPGENLILGFCLE<GDIDQDPSQNPFPEDKMDKGIYFTQ<VSEGGPAEIAGLQSGDKIMQVN

Parental  GWDMTMVTHDQARKRLTKRSEEVVRLLVTRQSLQKAVQQSML
          G.D.T...H.QA.K.LTK.SEEVVRLLVTRQSLQ.A.QQSM.
Retrocopy G*DVTVFPHHQAWKQLTKCSEEVVRLLVTRQSLQRAGQQSMV

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	41.81 RPM
SRP012922_cerebellum	0.00 RPM	4.67 RPM
SRP012922_heart	0.00 RPM	24.13 RPM
SRP012922_kidney	0.00 RPM	13.96 RPM
SRP012922_liver	0.00 RPM	9.75 RPM
SRP012922_lung	0.15 RPM	58.49 RPM
SRP012922_quadricep_muscle	0.00 RPM	6.40 RPM
SRP012922_spleen	0.00 RPM	29.65 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_2238 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000023829	1 retrocopy	retro_dnov_2238 ,
Myotis lucifugus	ENSMLUG00000026421	1 retrocopy	retro_mluc_221,
Sus scrofa	ENSSSCG00000017866	1 retrocopy	retro_sscr_365,
Ictidomys tridecemlineatus	ENSSTOG00000022920	1 retrocopy	retro_itri_134,