RetrogeneDB ID: retro_dnov_1293

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_17716:42018..42633(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TADA1
• Ensembl ID: ENSDNOG00000018606
• Aliases: None
• Description: transcriptional adaptor 1 [Source:HGNC Symbol;Acc:30631]

Sequence

>retro_dnov_1293
AGGCACACAAGTGACCAGTTGAGTAGTCTCATGGCTCATACCATGGTGATACTAAAGTTGTGATTTAAGCACAAGATCAG
CAAAGACGAATTTGACCTTGAAGCTCATAGACTTCACACACAGGATAACCTCCATTCACCATTTCTTCTTGGTCATTCTC
CCACTTTCTCAGATCATGGTTTCAACACCAGAGGGTGCTGGATCTTTACCCTGGAAAGGGGGTTCTGCAGACAAACCTGG
GAAACCCAAGGGAAAGAAAAAGCTTTCTTCAGTTCATCAGAGATTTGATTGCAGATTTCAGCTTCAAAATCCCCTCTCAG
GAGCCCAACAGTTTGTGGCAAAGCGTCCGCAAGATGATGACGACTTGAAACTTTGTCTCACATAATGATGCTTCCCACCC
AAGGTCAGCTTGAAGGGAGAATGGTAGTGACTGTTAAGGAGCATGAGTTGGACCACATCACCAGGGAGGCTGCCTCAGCT
GTTGTCGATGCAGTAGAGAATCACTTTAAAGATATTCTGACATGAGTTGTGTCAGGAAGGAAAGATTATTGGTTATGAGA
GTCACTTAAAATGTGTTTTGGTAGTAATGTGACTCCTCAGCCATACTTCAAGAGT

Alignment

ORF - retro_dnov_1293 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.52 %
• Parental protein coverage: 62.09 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KNLSEALGDNVKQYWANLKLWFKQKISKEEFDLEAHRLLTQDNVHSHNDFLLA-ILTRCQILVSTPEGAG
          ...S..L..........LKL.FK.KISK.EFDLEAHRL.TQDN...H..FLL..IL...QI.VSTPEGAG
Retrocopy RHTSDQLSSLMAHTMVILKL*FKHKISKDEFDLEAHRLHTQDNL--HSPFLLG>ILPLSQIMVSTPEGAG

Parental  SLPWTGGSAAKPGKPKGKKKLSSVRQKFDHRFQPQNPLSGAQQFVAKDPQDDDDLKLC-SHTMMLPTRGQ
          SLPW.GGSA.KPGKPKGKKKLSSV.Q.FD.RFQ.QNPLSGAQQFVAK.PQDDDDLKLC.SH.MMLPT.GQ
Retrocopy SLPWKGGSADKPGKPKGKKKLSSVHQRFDCRFQLQNPLSGAQQFVAKRPQDDDDLKLC<SHIMMLPTQGQ

Parental  LEGRMIVTAYEHGLDNVTEEAVSAVVYAVENHLKDILSSVVSRRKAYRLRDGHFKYAFGSNVTPQPYLKN
          LEGRM.VT..EH.LD..T.EA.SAVV.AVENH.KDIL..VVS.RK.Y.L.....K..FGSNVTPQPY.K.
Retrocopy LEGRMVVTVKEHELDHITREAASAVVDAVENHFKDILT*VVSGRKDYWL*ES-LKMCFGSNVTPQPYFKS

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	9.14 RPM
SRP012922_cerebellum	0.00 RPM	18.15 RPM
SRP012922_heart	0.00 RPM	6.03 RPM
SRP012922_kidney	0.00 RPM	9.31 RPM
SRP012922_liver	0.00 RPM	7.59 RPM
SRP012922_lung	0.15 RPM	17.87 RPM
SRP012922_quadricep_muscle	0.00 RPM	8.31 RPM
SRP012922_spleen	0.00 RPM	15.80 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_1293 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 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015607	1 retrocopy	retro_cfam_849,
Choloepus hoffmanni	ENSCHOG00000012658	1 retrocopy	retro_chof_602,
Cavia porcellus	ENSCPOG00000025598	1 retrocopy	retro_cpor_1225,
Dasypus novemcinctus	ENSDNOG00000018606	1 retrocopy	retro_dnov_1293 ,
Homo sapiens	ENSG00000152382	1 retrocopy	retro_hsap_3928,
Gorilla gorilla	ENSGGOG00000008168	1 retrocopy	retro_ggor_2644,
Mus musculus	ENSMUSG00000026563	1 retrocopy	retro_mmus_865,
Otolemur garnettii	ENSOGAG00000007621	1 retrocopy	retro_ogar_1989,
Pongo abelii	ENSPPYG00000000557	1 retrocopy	retro_pabe_3243,
Pan troglodytes	ENSPTRG00000001627	1 retrocopy	retro_ptro_2671,
Tupaia belangeri	ENSTBEG00000007283	1 retrocopy	retro_tbel_3501,