RetrogeneDB ID: retro_dnov_1484

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_214484:3174..3839(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM20B
• Ensembl ID: ENSDNOG00000006175
• Aliases: None
• Description: family with sequence similarity 20, member B [Source:HGNC Symbol;Acc:23017]

Sequence

>retro_dnov_1484
GTCACATATACCATGGCCACCAAGGAAATCATTAAAGCTGATGTATGTTTAGAGGGACACAATACTTGAAGCCTTACTAA
TACTTGAAGGAGGTCAGCAATTTGACGTCAAAACTAAGCAGTATAGATGAGGTTATGTGTTAGAAAGGAAACTATATGCC
CAGTTATGATAGACACAATGCAGAGGTAACAGTCTTTCATTAGGACAGGATTCTGGATTTCTGCCATGCCCCCTTTATGT
TTGGCAGATTTGGTAACATGTGGTCACAGGTCAAGTCTTTTGCCATGGAGCAGCTGCTGAGCACCTTTCTAACTGTGGGA
TTCAATACTTACTTCTATGGTAAGTGTTATCACTGCCAAGAAATAGAGCCAGCTTGTGCCAGTGGAGACTCAGTAGAGAA
ATCTATCACACTCTGGCTCCCGGATGTGTGGCCTCTTCAGAAACATGAATGTACCTGGGGCAGGGCTTACTGAGAGGGCA
AACTGGTCAGGTGGGATTGTGACAAGAGCTACCATGACACTGTGAAGGAAACATCTCCTTTTGACTCGGGCCTCCTGGAC
ACCATAGATACAGTTGTTTTTGATGATCTGACTGGCTATGCTGACTGCCATCACTACAAGAGCCTTCAAGATGACGAAGG
TGCTTTATCATTGGGGTATATAGAT

Alignment

ORF - retro_dnov_1484 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.56 %
• Parental protein coverage: 60.11 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IMHAMATKKIIKADVGYKG-TQLKALLILEGGQKVVFKPKRYSRDYVVEGEPYA-GYDRHNAEVAAFHLD
          ....MATK.IIKADV...G.T.L.ALLILEGGQ....K.K.Y...YV.E...YA..YDRHNAEV..FH.D
Retrocopy VTYTMATKEIIKADVCLEG>TILEALLILEGGQQFDVKTKQYR*GYVLERKLYA>SYDRHNAEVTVFH*D

Parental  RILGFRRAPLVVGRFVNLRTEIKPVATEQLLSTFLTVGNNTCFYGKCYYCRETEPACADGDTMEGSVTLW
          RIL.F..AP...GRF.N.....K..A.EQLLSTFLTVG.NT.FYGKCY.C.E.EPACA.GD..E.S.TLW
Retrocopy RILDFCHAPFMFGRFGNMWSQVKSFAMEQLLSTFLTVGFNTYFYGKCYHCQEIEPACASGDSVEKSITLW

Parental  LPDVWPLQKHRHPWGRTYREGKLARWEYDESYCDAVKKTSPYDSGPRLLDIIDTAVFDYLIGNADRHHYE
          LPDVWPLQKH...WGR.Y.EGKL.RW..D.SY.D.VK.TSP.DSG..LLD.IDT.VFD.L.G.AD.HHY.
Retrocopy LPDVWPLQKHECTWGRAY*EGKLVRWDCDKSYHDTVKETSPFDSG--LLDTIDTVVFDDLTGYADCHHYK

Parental  SFQDDEGASMLILLD
          S.QDDEGA..L...D
Retrocopy SLQDDEGALSLGYID

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	34.03 RPM
SRP012922_cerebellum	0.00 RPM	13.33 RPM
SRP012922_heart	0.00 RPM	7.43 RPM
SRP012922_kidney	0.00 RPM	17.52 RPM
SRP012922_liver	0.00 RPM	5.11 RPM
SRP012922_lung	0.00 RPM	17.87 RPM
SRP012922_quadricep_muscle	0.00 RPM	15.92 RPM
SRP012922_spleen	0.00 RPM	17.74 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_1484 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 13 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005236	6 retrocopies	retro_chof_1509, retro_chof_1926, retro_chof_2615, retro_chof_2629, retro_chof_799, retro_chof_868,
Dasypus novemcinctus	ENSDNOG00000006175	2 retrocopies	retro_dnov_1484 , retro_dnov_2346,
Echinops telfairi	ENSETEG00000005651	1 retrocopy	retro_etel_1128,
Homo sapiens	ENSG00000116199	1 retrocopy	retro_hsap_2730,
Gorilla gorilla	ENSGGOG00000002484	1 retrocopy	retro_ggor_1899,
Macropus eugenii	ENSMEUG00000006654	1 retrocopy	retro_meug_414,
Macaca mulatta	ENSMMUG00000006260	1 retrocopy	retro_mmul_1533,
Nomascus leucogenys	ENSNLEG00000015580	1 retrocopy	retro_nleu_592,
Otolemur garnettii	ENSOGAG00000012751	1 retrocopy	retro_ogar_2800,
Pongo abelii	ENSPPYG00000000466	2 retrocopies	retro_pabe_2268, retro_pabe_2269,
Pan troglodytes	ENSPTRG00000001725	1 retrocopy	retro_ptro_1845,
Ictidomys tridecemlineatus	ENSSTOG00000005086	2 retrocopies	retro_itri_441, retro_itri_539,
Tarsius syrichta	ENSTSYG00000005482	3 retrocopies	retro_tsyr_2065, retro_tsyr_2124, retro_tsyr_89,