RetrogeneDB ID: retro_dnov_1903

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_36098:4392..5547(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX17
• Ensembl ID: ENSDNOG00000006499
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box helicase 17 [Source:HGNC Symbol;Acc:2740]

Sequence

>retro_dnov_1903
ACCGAACCCACTGCTATTCAAGCTCAGGGATGGCCAGTTGCTCTTAGTGGATTGGATATGGTGGAGTAGCACAGACTGGA
TCTGGGAAAACGTTATCTTATTTGCTGCCTGCCCATTGTCCATATCAGTCATCAGCCATTCCTAGAGAGAGGTGATGGGC
CTATTTGCTTGGTGCTGGCACCAACTCGGGAACTGGCCCAACAAGTGCAGCAAGTAGCTGCCGAGTACTGTAGAGCATGT
TGCTTAAAGTCTACTTGTATCTATGGTGGTGCTCCCAAGGGACCACAAATACGTGATTTGGAAAGAGGTGTGGAAATCTG
TATTGCAACACCTGGAAGACTGATTGACTTTTTAGAGTGCGGGAAAACCAATTTGAGAAGAACAACCTATCTTGTCCTTG
ATGAAGCAGATAGAATGCTTGATATGGGCTTCGAACCCCAAATAAGGAAGATTGTGGATCAAATAAGACCTGATAGGCAA
ACTCTAATGTGGAGTGTGACTTGGCCAAAAGAAGTAAGACAGCTTGCTGAAGATTTCCTGAAAGACTATATTCATATAAA
CATTGGTGCACTAGAACTGAGTGCAAACCACAATATTCTTCAGATTGTAGATGTGTGTCATGATGTAGAAAAAGATGAAA
AACTTATTCGTCTAATGGAAGAAATCATGAGTGAGAAGGACAATACAACCATCGTTTTTGTGGAAACCAAAAGAAGATGT
GGTGAGTTTATCAGAAAAATGGAGAGAAATGGGTGGCCTGCCATGGGTATCCATGGTGACAAAAGTCAACAGGAACGTGA
CTGGGTTCTAAATGAATTCAAACATGGAAAAGCTCCTATTCTGATTGCTACAGATGTGGCCTCCAGAGGGCTAGATGTGG
AAGATGTGAAATTTGTCATCAGTTATGACTACCCTAACTCCTCAGAGGATTATATTCATCGAATTGGAAGAACTGCTCGC
AGTACCAAAACAGGCACAGCATACACTTTCTTTACACCTAATAACATAAAGCAAGTGAGCGACCTTATCTCTGTGCTTCG
TGAAGCCAATCAAGCAATTAATCCCAAGTTGCTTCAGTTGGTTGAAGACAGAGGTTCAGGTCGTTCCAGGGGTAGAGGAG
GCATGAAGGATGACCGTCGAGACAGATACTCTGCA

Alignment

ORF - retro_dnov_1903 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.88 %
• Parental protein coverage: 57.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TEPTPIQCQGFSLALSGRDMV-GIAQTGSGKTLAYLLPA-IVHINHQPYLERGDGPICLVLAPTRELAQQ
          TEPT.IQ.QG...ALSG.DMV.G.AQTGSGKTL.YLLPA.IVHI.HQP.LERGDGPICLVLAPTRELAQQ
Retrocopy TEPTAIQAQGWPVALSGLDMV<GVAQTGSGKTLSYLLPA>IVHISHQPFLERGDGPICLVLAPTRELAQQ

Parental  VQQVADDYGKCSRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLESGKTNLRRCTYLVLDEADR
          VQQVA..Y.....LKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLE.GKTNLRR.TYLVLDEADR
Retrocopy VQQVAAEYCRACCLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADR

Parental  MLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLRDYTQINVGNLELSANHNILQIVDVCME
          MLDMGFEPQIRKIVDQIRPDRQTLMWS.TWPKEVRQLAEDFL.DY..IN.G.LELSANHNILQIVDVC..
Retrocopy MLDMGFEPQIRKIVDQIRPDRQTLMWSVTWPKEVRQLAEDFLKDYIHINIGALELSANHNILQIVDVCHD

Parental  SEKDHKLIQLMEEIMAEKENKTIIFVETKRRCDDLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKA
          .EKD.KLI.LMEEIM.EK.N.TI.FVETKRRC....R.M.R.GWPAM.IHGDKSQ.ERDWVLNEF..GKA
Retrocopy VEKDEKLIRLMEEIMSEKDNTTIVFVETKRRCGEFIRKMERNGWPAMGIHGDKSQQERDWVLNEFKHGKA

Parental  PILIATDVASRGLDVEDVKFVINYDYPNSSEDYVHRIGRTARSTNKGTAYTFFTPGNLKQARELIKVLEE
          PILIATDVASRGLDVEDVKFVI.YDYPNSSEDY.HRIGRTARST..GTAYTFFTP.N.KQ...LI.VL.E
Retrocopy PILIATDVASRGLDVEDVKFVISYDYPNSSEDYIHRIGRTARSTKTGTAYTFFTPNNIKQVSDLISVLRE

Parental  ANQAINPKLMQLVDHRGGG---GGGGGRSRYRTTSSA
          ANQAINPKL.QLV..RG.G...G.GG.....R...SA
Retrocopy ANQAINPKLLQLVEDRGSGRSRGRGGMKDDRRDRYSA

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	219.94 RPM	198.55 RPM
SRP012922_cerebellum	260.92 RPM	211.29 RPM
SRP012922_heart	86.55 RPM	50.12 RPM
SRP012922_kidney	144.02 RPM	47.64 RPM
SRP012922_liver	140.10 RPM	81.43 RPM
SRP012922_lung	346.99 RPM	165.25 RPM
SRP012922_quadricep_muscle	42.92 RPM	51.41 RPM
SRP012922_spleen	314.20 RPM	229.04 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_1903 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006499	1 retrocopy	retro_dnov_1903 ,
Otolemur garnettii	ENSOGAG00000001539	1 retrocopy	retro_ogar_3395,
Rattus norvegicus	ENSRNOG00000013691	1 retrocopy	retro_rnor_1276,