RetrogeneDB ID: retro_dnov_1374

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_18939:47659..48302(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4E2
• Ensembl ID: ENSDNOG00000016877
• Aliases: None
• Description: eukaryotic translation initiation factor 4E family member 2 [Source:HGNC Symbol;Acc:3293]

Sequence

>retro_dnov_1374
TTGAAAGATAATGACGGTGGGGACCATGATCAGAATGATAAAACGGCACACAGAAAGATGATGAGAAGGAAAAAACGGAA
TGAGACATTAGTCAGAGCAGCAGCAAGAGGAAAGCTGTTGTCCCTGGACCAGCAGAACATCCCTTGCAGTACAACTACAC
TTTCTGATACTGTAGGAGAACTCTTGGCCACCCCACCAGCTCACAGAGCTATGAACAGAATATTAAGCAGATAGGCACCT
TCACCTCTGTGGAGCAGTTCTGGAGGTTTTACAACCATATGGTGCTCCTGAAGACCTGAGAGGCCACAGTGACTTCCATC
GCTTCAGAGAAGGAGTTAAGCCCATGTGGAAGGATGATGCAAATAAAAATGGTGGCAAGTGCTTTTTTTGGCTGAGGAAG
GGCTTGGCATCCCGTTGCTGGGAGAATCTCATCCTGGCCATGTTGGGGGAGCAGTTCATGGTTGGGGAGGAGATCTGTGG
GGCTGTGGTCTCTGTCTGGTTTCAGGAGGACAATATTTCAATATGGAACAAGACAGCCACTGACAAAGCAACTACAGCCT
GAATCCAGGACATGCTTCGGCAAGTGCTTAACCTAACTCCCAACACCACTATGGAATACAAAACCCACACTGACCGCATC
AAG

Alignment

ORF - retro_dnov_1374 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.95 %
• Parental protein coverage: 90.34 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LKDDDSGDHDQNEE-NSTQKDGEKEKTERDKSQSSSKRKAVVPGPAEHPLQYNYTFWYSRRTPGRPTSSQ
          LKD.D.GDHDQN...N.TQKD.EKEKTE.D.SQSSSKRKAVVPGPAEHPLQYNYTF.Y.RRT.G.PTSSQ
Retrocopy LKDNDGGDHDQNDK<NGTQKDDEKEKTE*DISQSSSKRKAVVPGPAEHPLQYNYTF*YCRRTLGHPTSSQ

Parental  SYEQNIKQIGTFASVEQFWRFYSHMV-RPGDLTGHSDFHLFKEGVKPMWEDDANKNGGKWIIRLRKGLAS
          SYEQNIKQIGTF.SVEQFWRFY.HMV..P.DL.GHSDFH.F.EGVKPMW.DDANKNGGK....LRKGLAS
Retrocopy SYEQNIKQIGTFTSVEQFWRFYNHMV<APEDLRGHSDFHRFREGVKPMWKDDANKNGGKCFFWLRKGLAS

Parental  RCWENLILAMLGEQFMVGEEICGAVVSVRFQEDIISIWNKTASDQATTARIRDTLRRVLNLPPNTIMEYK
          RCWENLILAMLGEQFMVGEEICGAVVSV.FQED.ISIWNKTA.D.ATTA.I.D.LR.VLNL.PNT.MEYK
Retrocopy RCWENLILAMLGEQFMVGEEICGAVVSVWFQEDNISIWNKTATDKATTA*IQDMLRQVLNLTPNTTMEYK

Parental  THTDSIK
          THTD.IK
Retrocopy THTDRIK

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	0.39 RPM	25.86 RPM
SRP012922_cerebellum	0.00 RPM	13.33 RPM
SRP012922_heart	0.00 RPM	10.91 RPM
SRP012922_kidney	0.00 RPM	13.14 RPM
SRP012922_liver	0.15 RPM	11.30 RPM
SRP012922_lung	0.46 RPM	23.06 RPM
SRP012922_quadricep_muscle	0.00 RPM	8.31 RPM
SRP012922_spleen	0.23 RPM	21.40 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_1374 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011328	1 retrocopy	retro_cfam_183,
Callithrix jacchus	ENSCJAG00000013786	2 retrocopies	retro_cjac_1061, retro_cjac_2717,
Dasypus novemcinctus	ENSDNOG00000013712	5 retrocopies	retro_dnov_1722, retro_dnov_2378, retro_dnov_2570, retro_dnov_353, retro_dnov_638,
Dasypus novemcinctus	ENSDNOG00000016877	1 retrocopy	retro_dnov_1374 ,
Microcebus murinus	ENSMICG00000015082	2 retrocopies	retro_mmur_806, retro_mmur_975,
Myotis lucifugus	ENSMLUG00000011269	1 retrocopy	retro_mluc_60,
Otolemur garnettii	ENSOGAG00000009155	1 retrocopy	retro_ogar_104,
Sarcophilus harrisii	ENSSHAG00000013108	1 retrocopy	retro_shar_101,