RetrogeneDB ID: retro_dnov_894

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_118763:239..824(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FKBP4
• Ensembl ID: ENSDNOG00000011244
• Aliases: None
• Description: FK506 binding protein 4, 59kDa [Source:HGNC Symbol;Acc:3720]

Sequence

>retro_dnov_894
AAGGAGAATGCCACTTTTGGTGTTGGGAAGGAAAAGTTCCAGATGCCACCATAGGCTGTGCTGAAATGTGAAGCGTATCT
CGAAAGAGTTTGAGAAAGCCAGGGATTCTTATGAGATGAGTTTGGAGGTGGAGCTGGAATAGAGAGACATGGTGAAAGAA
CAGAGAACAGTGTACCTCAAGGAAGACAAGTTAAGCAAGCTTTTCTGCAGTAAGAGAAGACTATCCTGGCTGGAGTATGG
AAGGAGTTTCTCCCATGAGGAAGCACAGAAAGCACAGGCCCTTCCACTGGCCTCCCACCTCAATCTGGCCATGTGTCATT
GAAGCTACAGGCCTTCTCAACTGCCACTGAAAAGTGCAACAAAGCCCTGAAAGGACAGCAACAACAAGAAGGGCCTCTTC
TACCAGGGAGAGGCCCACCTGGTAGAAATGAATTTGACCTACCACAATCTGACTTCCAGAAGGTTCTGAAGCTCTACCTT
AGCAACAAGGCCCAGCTGGTTGCCTACCAGCAGCAGGTCTGCAAGGAGCTCACAAGGGAGAAGCAGCTCTTTGCCAACAT
GTTTGAGAGGCTGGCTGAGGGGGAG

Alignment

ORF - retro_dnov_894 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.14 %
• Parental protein coverage: 51.8 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KPSYAFGSLGKEKFQIPPEAELKYKVHL-KSFEKAKESWEMSSEEKLEQSAIVKERGTVYFKEGKYKQAV
          K....FG..GKEKFQ.PP.A.LK....L.K.FEKA..S.EMS.E..LE....VKE..TVY.KE.K.....
Retrocopy KENATFG-VGKEKFQMPP*AVLKCEAYL>KEFEKARDSYEMSLEVELE*RDMVKEQRTVYLKEDKLSKLF

Parental  LQYKKIVSWLEYESSFSTEEVQKAQALRLASHLNLAMCY-LKLQAFSAAIENCNKALELDGNNEKGLFRR
          ...K...SWLEY..SFS.EE.QKAQAL.LASHLNLAMC..LKLQAFS.A.E.CNKAL........G....
Retrocopy CS-KRRLSWLEYGRSFSHEEAQKAQALPLASHLNLAMCH<LKLQAFSTATEKCNKALK-GQQQQEGPLLP

Parental  GEAHLAVNDFDLARADFQKVLQLYPSNKAAKAQLVICQQRIRKQLAREKKLYANMFERLAEEE
          G......N.FDL...DFQKVL.LY.SNKA...QLV..QQ...K.L.REK.L.ANMFERLAE.E
Retrocopy GRGPPGRNEFDLPQSDFQKVLKLYLSNKA---QLVAYQQQVCKELTREKQLFANMFERLAEGE

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	71.95 RPM
SRP012922_cerebellum	0.00 RPM	74.51 RPM
SRP012922_heart	0.00 RPM	18.10 RPM
SRP012922_kidney	0.00 RPM	115.27 RPM
SRP012922_liver	0.00 RPM	94.90 RPM
SRP012922_lung	0.00 RPM	54.52 RPM
SRP012922_quadricep_muscle	0.00 RPM	15.92 RPM
SRP012922_spleen	0.00 RPM	58.49 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_894 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 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007605	1 retrocopy	retro_btau_561,
Callithrix jacchus	ENSCJAG00000018746	1 retrocopy	retro_cjac_436,
Dasypus novemcinctus	ENSDNOG00000004678	1 retrocopy	retro_dnov_1280,
Dasypus novemcinctus	ENSDNOG00000005868	16 retrocopies	retro_dnov_1289, retro_dnov_1577, retro_dnov_1666, retro_dnov_2236, retro_dnov_228, retro_dnov_2404, retro_dnov_2418, retro_dnov_2544, retro_dnov_2589, retro_dnov_263, retro_dnov_584, retro_dnov_621, retro_dnov_670, retro_dnov_684, retro_dnov_707, retro_dnov_937,
Dasypus novemcinctus	ENSDNOG00000011244	1 retrocopy	retro_dnov_894 ,
Homo sapiens	ENSG00000004478	5 retrocopies	retro_hsap_3085, retro_hsap_4162, retro_hsap_4165, retro_hsap_4264, retro_hsap_4266,
Gorilla gorilla	ENSGGOG00000010471	4 retrocopies	retro_ggor_2120, retro_ggor_2852, retro_ggor_2854, retro_ggor_2855,
Macaca mulatta	ENSMMUG00000007405	1 retrocopy	retro_mmul_1969,
Nomascus leucogenys	ENSNLEG00000002835	1 retrocopy	retro_nleu_2291,
Pongo abelii	ENSPPYG00000004149	4 retrocopies	retro_pabe_2607, retro_pabe_2611, retro_pabe_3383, retro_pabe_3518,
Pan troglodytes	ENSPTRG00000004529	3 retrocopies	retro_ptro_2083, retro_ptro_3000, retro_ptro_3001,