RetrogeneDB ID: retro_dnov_66

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_1202:36337..36872(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STYX
• Ensembl ID: ENSDNOG00000016631
• Aliases: None
• Description: serine/threonine/tyrosine interacting protein [Source:HGNC Symbol;Acc:11447]

Sequence

>retro_dnov_66
GAAGAGTCGACCTATCCAAAGAGAGAAGAAATGCAGGACGTTTTACCTGAATTTTTAGACCCATATTCATCTGCTATGAA
AAGCAAGCTACCTGTACTACAGAAACATAGAATAATAACCCCTATAATATACATGAAACAAAATATTGACGCAAACTTTA
TTAAACCAAACTTTTAGCAATTATTTAGATATTTAGTCTTGTATATTGCAGATAATCCAGTTGAAAATATAATACTTTTT
TTGCCCATGACTAAAAGAATTTATTGATGGGAGCTTCCAACCTGGAGGAAAAGTTTTAGTCCATGGAAATGCAGGGATCT
CCAGGAATGCTACCTTTTGTTATTGCAAACATTATGGGAAACATTTAGAATGAAAGACAGAGATACATTTTGCCTACGTT
CAAGAAAGAAGATTTTGCATTAATTCAATGCTGGATTTGTCCATGGTTTTAGTAATATGAAGCCATTGACCTAGGAAAAT
TAAATATACAAGTGATGTCACCACTACAGGTAGGAGGTTATTATCTGTCCCTTCG

Alignment

ORF - retro_dnov_66 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.19 %
• Parental protein coverage: 79.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  EEWTYPMRREMQEILPGLFLGPYSSAMKSKLPILQKHGI-THIICIRQNIEANFIKPNFQQLFRYLVLDI
          EE.TYP.R.EMQ..LP..FL.PYSSAMKSKLP.LQKH.I.T.II...QNI.ANFIKPNF.QLFRYLVL.I
Retrocopy EESTYPKREEMQDVLPE-FLDPYSSAMKSKLPVLQKHRIITPIIYMKQNIDANFIKPNF*QLFRYLVLYI

Parental  ADNPVENIIRFFPMTK-EFIDGSFQTGGKVLVHGNAGISRSAA-FVIAYIM-ETFGMKYRDA-FAYVQER
          ADNPVENII.F.PMTK.EFIDGSFQ.GGKVLVHGNAGISR.A..FVIA.IM.ETF.MK.RD..FAYVQER
Retrocopy ADNPVENIILFLPMTK>EFIDGSFQPGGKVLVHGNAGISRNAT>FVIANIM>ETFRMKDRDT>FAYVQER

Parental  RFCINP-NAGFVHQLQE-YEAIYLAKLTIQMMSPVQI-ERSLSVHS
          RFCIN..NAGFVH.....YEAI.L.KL.IQ.MSP.Q...R.LSV.S
Retrocopy RFCINS<NAGFVHGFSN<YEAIDLGKLNIQVMSPLQV<RRLLSVPS

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	6.03 RPM
SRP012922_cerebellum	0.69 RPM	3.44 RPM
SRP012922_heart	0.23 RPM	4.64 RPM
SRP012922_kidney	0.00 RPM	4.93 RPM
SRP012922_liver	0.00 RPM	2.63 RPM
SRP012922_lung	0.76 RPM	4.89 RPM
SRP012922_quadricep_muscle	0.35 RPM	11.77 RPM
SRP012922_spleen	0.69 RPM	5.61 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_66 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 8 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000016631	9 retrocopies	retro_dnov_1713, retro_dnov_1720, retro_dnov_1914, retro_dnov_2138, retro_dnov_2186, retro_dnov_2218, retro_dnov_2221, retro_dnov_461, retro_dnov_66 ,
Echinops telfairi	ENSETEG00000000561	1 retrocopy	retro_etel_1881,
Monodelphis domestica	ENSMODG00000029372	1 retrocopy	retro_mdom_44,
Mus musculus	ENSMUSG00000053205	1 retrocopy	retro_mmus_96,
Ochotona princeps	ENSOPRG00000016123	1 retrocopy	retro_opri_976,
Rattus norvegicus	ENSRNOG00000007956	1 retrocopy	retro_rnor_256,
Ictidomys tridecemlineatus	ENSSTOG00000014504	1 retrocopy	retro_itri_1365,
Vicugna pacos	ENSVPAG00000012229	1 retrocopy	retro_vpac_464,