RetrogeneDB ID: retro_dnov_618

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_6854:535353..536324(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IK
• Ensembl ID: ENSDNOG00000009727
• Aliases: None
• Description: IK cytokine, down-regulator of HLA II [Source:HGNC Symbol;Acc:5958]

Sequence

>retro_dnov_618
GAACTGTTCTCCAACCCTTTGGTGCCAGATGGCCATGTTGTAGACGATGCTCACTCCTGCCACCAATAAAACTCACCAAT
GAAGACTTCAGGAGGCTTCTCATGACCCCAAGGGCAGCACCCACCTCTGCAACACCCTCTAAGTCAGTCACCACGAGATG
CCAAGGGAGTACAATGAGGATGAAGACCCAGCTGTGCAAAGAAGGAAAAAGAAAAGTTATTTATACCAAGCTCTGCCAAC
AAAAAATTGAAAGACAGCGGGAGCTAGCAGAGAAGTACCGGGACCATGCCAAGGAACAGAGAGATGGGGTGAACAAAGAT
TATGAGGAAACTGAACTCATCAGTACCACAGTTAACTACAGAGCTGTGGGCCCCACTGCTGAGGTGGACAAATCAGCTGC
AGAGAAGAGAAGACAGTTGATCTGGGAGTCCAAATTCTTGGGTGGTGATATGGAACACACCCATTCGGTGAAAGGCTTGG
ATTTTGCTCTGCTTCAGAAGGTACGAGCTGAGATTGCCAGCAAAGAAAAAGAGGAGGAAGAACTGATGGAAAAACCCCAA
AAGGAAACCAAGAAAGATGAAGATCCTGAGAACAAGATTGAATTTAAAACATGCCTGGGCCGCAATGTTTATCGTATACT
CTTCAAGAGCCAAGCATATGAGAGGAACGAGCTGTTCCTGCCGGGTCTCATGGCCTACGTGGTGGACTTGGATGATGAGT
TTGCCAACACAGACATCCCCACCACTCTTATTTGCAGCAAGGCTGATTGCCCCACCATGGAGGCCCAGACCACACTGACC
ACAAATGACATTGTCATCAGTAAGCTCACCCAGATCCTTTCCTACCTGAGGCAGGGTACCCGCAACAAGAAGCTCAAGAA
GAAAGATAAAGGGAAGTTGGAAGAGAAGAAACCTCTTGAGGCTGACATAAACATTTTTGAAGACATTGGCGATTATGTGC
CCTCCACGACC

Alignment

ORF - retro_dnov_618 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.91 %
• Parental protein coverage: 58.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EPFSNPLAPDGHDVDDPHSFHQ-SKLTNEDFRKLLMTPRAAPTSAPPSKS-RHHEMPREYNEDEDPAARR
          E.FSNPL.PDGH.VDD.HS.HQ..KLTNEDFR.LLMTPRAAPTSA.PSKS..HHEMPREYNEDEDPA..R
Retrocopy ELFSNPLVPDGHVVDDAHSCHQ<IKLTNEDFRRLLMTPRAAPTSATPSKS<SHHEMPREYNEDEDPAVQR

Parental  RKKKSY-YAKLRQQEIERERELAEKYRDRAKERRDGVNKDYEETELISTTANYRAVGPTAEADKSAAEKR
          RKKKSY.Y.KL.QQ.IER.RELAEKYRD.AKE.RDGVNKDYEETELISTT.NYRAVGPTAE.DKSAAEKR
Retrocopy RKKKSY>YTKLCQQKIERQRELAEKYRDHAKEQRDGVNKDYEETELISTTVNYRAVGPTAEVDKSAAEKR

Parental  RQLIQESKFLGGDMEHTHLVKGLDFALLQKVRAEIASKEKEEEELMEKPQKETKKDEDPENKIEFKTRLG
          RQLI.ESKFLGGDMEHTH.VKGLDFALLQKVRAEIASKEKEEEELMEKPQKETKKDEDPENKIEFKT.LG
Retrocopy RQLIWESKFLGGDMEHTHSVKGLDFALLQKVRAEIASKEKEEEELMEKPQKETKKDEDPENKIEFKTCLG

Parental  RNVYRMLFKSKAYERNELFLPGRMAYVVDLDDEYADTDIPTTLIRSKADCPTMEAQTTLTTNDIVISKLT
          RNVYR.LFKS.AYERNELFLPG.MAYVVDLDDE.A.TDIPTTLI.SKADCPTMEAQTTLTTNDIVISKLT
Retrocopy RNVYRILFKSQAYERNELFLPGLMAYVVDLDDEFANTDIPTTLICSKADCPTMEAQTTLTTNDIVISKLT

Parental  QILSYLRQGTRNKKLKKKDKGKLEEKKPPEADMNIFEDIGDYVPSTT
          QILSYLRQGTRNKKLKKKDKGKLEEKKP.EAD.NIFEDIGDYVPSTT
Retrocopy QILSYLRQGTRNKKLKKKDKGKLEEKKPLEADINIFEDIGDYVPSTT

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	1.17 RPM	92.76 RPM
SRP012922_cerebellum	1.79 RPM	131.01 RPM
SRP012922_heart	0.70 RPM	46.17 RPM
SRP012922_kidney	1.37 RPM	79.40 RPM
SRP012922_liver	0.77 RPM	61.61 RPM
SRP012922_lung	2.14 RPM	125.23 RPM
SRP012922_quadricep_muscle	0.35 RPM	44.66 RPM
SRP012922_spleen	1.60 RPM	131.52 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_618 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009727	3 retrocopies	retro_dnov_618 , retro_dnov_714, retro_dnov_960,
Dipodomys ordii	ENSDORG00000006584	4 retrocopies	retro_dord_128, retro_dord_130, retro_dord_134, retro_dord_139,
Homo sapiens	ENSG00000113141	1 retrocopy	retro_hsap_2262,
Gorilla gorilla	ENSGGOG00000013374	1 retrocopy	retro_ggor_1685,
Loxodonta africana	ENSLAFG00000008152	1 retrocopy	retro_lafr_362,
Otolemur garnettii	ENSOGAG00000014281	1 retrocopy	retro_ogar_1402,
Pongo abelii	ENSPPYG00000015861	1 retrocopy	retro_pabe_1954,
Sorex araneus	ENSSARG00000007388	3 retrocopies	retro_sara_416, retro_sara_419, retro_sara_558,