RetrogeneDB ID: retro_dnov_268

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_3155:273124..273557(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF5A2
• Ensembl ID: ENSDNOG00000014801
• Aliases: None
• Description: eukaryotic translation initiation factor 5A2 [Source:HGNC Symbol;Acc:3301]

Sequence

>retro_dnov_268
ATGGCAGATGATTTGGACTTTGAGAGAGGAGATAAGGTGCTTCAGCCACCTCCCAAAGCAGTGCTTGGCGTTACGTAAGA
AAGGCTTTGTGGTGCTCAAAGAGCAGCCACGTAGGATTGTTGAGATGCCTACTGCCAAGACTGGCCAGCATAGCCACGCC
AGGGTTCACCTGGTTGGTATCGAGATCTTTACTGGGAAGAAATATGGAGCTATCTGCCCCTCAACTTATAATATGGATGT
CCCCAACATCAAAAGGAAGGACTTCCAGCGGACTGACATCCAGAATGGGTATCTATCGCTGCTCCAGGGCAGCGGGGAGG
TGAGGGAGGACCTTCGTCTGCCTGAGGGAGACCTTGGCCAGGAGACTGAACTGCGAAGTGATGCTGAGCACGGTGCGGTG
GCCGTGACAGAGGAGGCAGCTGCTGCAATACAG

Alignment

ORF - retro_dnov_268 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.91 %
• Parental protein coverage: 98.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADEIDFTTGDA-GASST-YPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKK
          MAD..DF..GD..GAS.T..P.QC.ALRK.GFVVLK..P..IVEM.T.KTG.H.HA.VHLVGI.IFTGKK
Retrocopy MADDLDFERGDK<GASAT<LPKQCLALRKKGFVVLKEQPRRIVEMPTAKTGQHSHARVHLVGIEIFTGKK

Parental  YEDICPSTHNMDVPNIKRNDYQLICIQDGYLSLLTETGEVREDLKLPEGELGKEIEGKYNAGEDVQSAMC
          Y..ICPST.NMDVPNIKR.D.Q...IQ.GYLSLL...GEVREDL.LPEG.LG.E.E....A.........
Retrocopy YGAICPSTYNMDVPNIKRKDFQRTDIQNGYLSLLQGSGEVREDLRLPEGDLGQETELRSDA----EHGAV

Parental  AMSEEYAVAIK
          A..EE.A.AI.
Retrocopy AVTEEAAAAIQ

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	3.89 RPM
SRP012922_cerebellum	0.00 RPM	2.34 RPM
SRP012922_heart	0.00 RPM	0.23 RPM
SRP012922_kidney	0.00 RPM	0.55 RPM
SRP012922_liver	0.00 RPM	0.00 RPM
SRP012922_lung	0.00 RPM	1.37 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.35 RPM
SRP012922_spleen	0.00 RPM	1.49 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_268 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005363	1 retrocopy	retro_chof_1016,
Cavia porcellus	ENSCPOG00000012594	1 retrocopy	retro_cpor_1060,
Dasypus novemcinctus	ENSDNOG00000014801	2 retrocopies	retro_dnov_1133, retro_dnov_268 ,
Homo sapiens	ENSG00000163577	1 retrocopy	retro_hsap_1591,
Loxodonta africana	ENSLAFG00000013225	1 retrocopy	retro_lafr_901,
Macropus eugenii	ENSMEUG00000007473	2 retrocopies	retro_meug_1619, retro_meug_641,
Macaca mulatta	ENSMMUG00000022880	1 retrocopy	retro_mmul_2222,
Nomascus leucogenys	ENSNLEG00000005292	1 retrocopy	retro_nleu_1762,
Oryctolagus cuniculus	ENSOCUG00000016657	1 retrocopy	retro_ocun_65,
Pongo abelii	ENSPPYG00000014294	2 retrocopies	retro_pabe_1308, retro_pabe_1640,
Pan troglodytes	ENSPTRG00000015621	1 retrocopy	retro_ptro_1070,
Ictidomys tridecemlineatus	ENSSTOG00000008130	2 retrocopies	retro_itri_1400, retro_itri_689,
Tupaia belangeri	ENSTBEG00000000408	2 retrocopies	retro_tbel_1442, retro_tbel_4419,