RetrogeneDB ID: retro_dnov_2190

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_54229:7785..8811(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KLHL12
• Ensembl ID: ENSDNOG00000010436
• Aliases: None
• Description: kelch-like family member 12 [Source:HGNC Symbol;Acc:19360]

Sequence

>retro_dnov_2190
TTAACTGCCTCTACCATGGAAATCCTTTTGGGTTTTGTGTACAAAGAAACAGTACGTGTGACAATGGAGAATGTACAGGA
ACGGCTCCCTGTGGCCTGTCTGCTTCAGCTGAAAGGTGTGAAGCAAGCCTGCTGTGAGTTTTTAGAAAGTCTGTTGGGCC
CTTCTAATTGCCTGGGTGTCAGGGATTTTGCCGTAACTAAAAATTCTGTTGACCTGATGCAAGCAGCTGAGGTTTTTAGC
CAGAAGCATTTTCCTGAAATGGTACAGTATGAAGAATGCATTCTTCTAAGTCAAGGAAAGGAGGAAAAGCTAATGAAGTG
TAATGAAATTCAAGTGGATCCTGAGCCTGGCTTTGAGGCTGTCATCAGTTGGGGGAAACATGCCAAGAAGGAACGAGAAG
AATCCTTGCCTGGCATGCTACAGTATGTAGGAATGCCCCTGCTGACTCCTAGGTGGATCACAGATGTAACAGATGCTGGG
CCTTTCATCCACTATAGTTTACAACCCAGGGACCTAGTTGATAAAGCAAAGAAGTTCCATCTGAGCTGAACTGTGGAGTC
AGATGCAAGGACCCAAGACAAGTGCTCCTCTAGGAGCCAATGAAGTGCTTCTGGTAATTGGGAGCTTCAGAAGTTAGCAG
TCTCCCTTTGACATGGTAGAGAAATATGACCCCAAAACTCAAGAGTGGAGCTTTTTGCCAAGCATCACTTAAAAGAGATG
ATATGCAGCTTCAGTGTCCCTACACAACCGGATCTATGTAACTGGTGGCTATGACGGCTGTTCTCGCCTCAGTTCAGTGG
AATATCTAGACTGCACAGCAGATGAGGATGGAATCTGGAATTCTGTGGCCCCTGTGAATGTTTGATGAAGGCTTGCTAGA
GCTACCACCCTAGGAGATATCTATGTATCTGGAGACTTTGATGAAAGCAGATGTCATACTGGTTTGGAGCAATATGACCC
AAACTTTGACCAATGGAGCATGCTGGGAGATATGCAGACAGCCGGGAAGGTGCCGACTTGCCAGTG

Alignment

ORF - retro_dnov_2190 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.3 %
• Parental protein coverage: 60.74 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LTASTMEILLDFVYTETVHVTVENVQELLPAACLLQLKGVKQACCEFLESQLDPSNCLGIRDFAETHNCV
          LTASTMEILL.FVY.ETV.VT.ENVQE.LP.ACLLQLKGVKQACCEFLES.L.PSNCLG.RDFA.T.N.V
Retrocopy LTASTMEILLGFVYKETVRVTMENVQERLPVACLLQLKGVKQACCEFLESLLGPSNCLGVRDFAVTKNSV

Parental  DLMQAAEVFSQKHFPEVVQHEEFILLSQGEVEKLIKCDEIQVDSEEPVFEAVINWVKHAKKEREESLPDL
          DLMQAAEVFSQKHFPE.VQ.EE.ILLSQG..EKL.KC.EIQVD..EP.FEAVI.W.KHAKKEREESLP..
Retrocopy DLMQAAEVFSQKHFPEMVQYEECILLSQGKEEKLMKCNEIQVD-PEPGFEAVISWGKHAKKEREESLPGM

Parental  LQYVRMPLLTPRYITDVIDAEPFIRCSLQCRDLVDEAKKFHLRPELRS-QMQGPR-TRARLGANEVLLVV
          LQYV.MPLLTPR.ITDV.DA.PFI..SLQ.RDLVD.AKKFHL.....S.....PR.T.A.LGANEVLLV.
Retrocopy LQYVGMPLLTPRWITDVTDAGPFIHYSLQPRDLVDKAKKFHLS*TVES<RCKDPR<TSAPLGANEVLLVI

Parental  GGFGSQQSPIDVVEKYDPKTQEWSFLPSITRKRRYVASVSLHDRIYVIGGYDGRSRLSSVECLDYTADED
          G.F.S.QSP.D.VEKYDPKTQEWSFLPSIT.KR.Y.ASVSLH.RIYV.GGYDG.SRLSSVE.LD.TADED
Retrocopy GSFRS*QSPFDMVEKYDPKTQEWSFLPSIT*KR*YAASVSLHNRIYVTGGYDGCSRLSSVEYLDCTADED

Parental  GVWYSVAPMNVRRGLAGATTLGDMIYVSGGFDGSRRHTSMERYDPNIDQWSMLGDMQTA-REGAGLVV
          G.W.SVAP.NV...LA.ATTLGD.IYVSG.FD.SR.HT..E.YDPN.DQWSMLGDMQTA.REGA.L.V
Retrocopy GIWNSVAPVNV**RLARATTLGD-IYVSGDFDESRCHTGLEQYDPNFDQWSMLGDMQTA<REGADLPV

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	35.78 RPM
SRP012922_cerebellum	0.00 RPM	25.98 RPM
SRP012922_heart	0.00 RPM	8.82 RPM
SRP012922_kidney	0.00 RPM	22.18 RPM
SRP012922_liver	0.00 RPM	7.90 RPM
SRP012922_lung	0.00 RPM	18.79 RPM
SRP012922_quadricep_muscle	0.00 RPM	13.85 RPM
SRP012922_spleen	0.00 RPM	33.31 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_2190 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006231	1 retrocopy	retro_cjac_2151,
Dasypus novemcinctus	ENSDNOG00000010436	1 retrocopy	retro_dnov_2190 ,
Echinops telfairi	ENSETEG00000007800	2 retrocopies	retro_etel_2103, retro_etel_723,
Homo sapiens	ENSG00000117153	1 retrocopy	retro_hsap_2545,
Macaca mulatta	ENSMMUG00000017849	1 retrocopy	retro_mmul_612,
Nomascus leucogenys	ENSNLEG00000018103	1 retrocopy	retro_nleu_2795,
Otolemur garnettii	ENSOGAG00000014771	1 retrocopy	retro_ogar_1552,
Pongo abelii	ENSPPYG00000000343	1 retrocopy	retro_pabe_1872,
Pan troglodytes	ENSPTRG00000001861	1 retrocopy	retro_ptro_1483,