RetrogeneDB ID: retro_dnov_1433

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_203333:3252..4029(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPK
• Ensembl ID: ENSDNOG00000000026
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein K [Source:HGNC Symbol;Acc:5044]

Sequence

>retro_dnov_1433
TTGCAGTTGCCATTACCCACTGCAACCAGCCAGCTCCCACTCAGATCTGATGCTGTGGGATGCTTCAATTATCAACACTG
TAAAGGAAGCGACTTTGACAAGAAACTATCGATTCATCAGAGTCTGGCAAAAGGAATTTTGGGGGTCAAAGGTACTAAAA
TGAAAGAACTCTGAGAGAACACTCAGACAACAATCAAACTTTTCTAGGACTGCTGTCCTCATTCCACTGACAGAGTCATT
CTTATTGAAGGAAATTCTGATAGGGTTGTAGAGTGCATAAAGATTATCCTTAATTTTATGTCTGAATCTCCCATCAAAGG
ATGTGCACAGCCTTATGATCCCATTGTTTATGATGAAACCTATGATTATGATGGTTTTACAATGATGTTTGATGACCACT
GTGGATACCCTGTGGGATTTCCCATACTGGGAAGAAGTGGTTTTGACAGAATGCCTCCTGGTGAGGGTGGGTGTCCAATG
CCTCCATCTAGAAGAGACTATGATGATATGAGCACTCATCAAGGACTTCCTCCTCCTCTTCCTCAATGAGGTGGGAGGTG
GAAGTAGAGCTTGGAATCTTCCTCTTCCCCCACCATCACCACCACCACCTAGAGGAGGAGATCTAACGACTTATGACAGC
AGAGGAAGACCTGAGGACTGTTACAATGGCATGGTTGGTTTCACTGCTGATGAAACTTGGACTCTGCAATAGAAACATGG
AGCCCATCACAATGGCAGGTGGCTTATGAACCACAGGGTGGCTCTATATATGATTAC

Alignment

ORF - retro_dnov_1433 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.52 %
• Parental protein coverage: 66.16 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LQLPSPTATSQLPLESDAVECLNYQHYKGSDFDCELRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLF
          LQLP.PTATSQLPL.SDAV.C.NYQH.KGSDFD....L.IHQSLA.GI.GVKG.K.KEL.ENTQTTIKLF
Retrocopy LQLPLPTATSQLPLRSDAVGCFNYQHCKGSDFD--KKLSIHQSLAKGILGVKGTKMKEL*ENTQTTIKLF

Parental  QECCPHSTDRVVLIGGKPDRVVECIKIILDLISESPIKGRAQPYDPNFYDETYDYGGFTMMFDDRRGRPV
          ..CCPHSTDRV.LI.G..DRVVECIKIIL...SESPIKG.AQPYDP..YDETYDY.GFTMMFDD..G.PV
Retrocopy *DCCPHSTDRVILIEGNSDRVVECIKIILNFMSESPIKGCAQPYDPIVYDETYDYDGFTMMFDDHCGYPV

Parental  GFPMRGRGGFDRMPPGRGGRPMPPSRRDYDDMSPRRGPPPPPPGRGGR-GGSRARNLPLPP--PPPPRGG
          GFP..GR.GFDRMPPG.GG.PMPPSRRDYDDMS...G.P.PP....G..GGSRA.NLPLPP..PPPPRGG
Retrocopy GFPILGRSGFDRMPPGEGGCPMPPSRRDYDDMSTHQGLP-PPLPQ*GG>GGSRAWNLPLPPPSPPPPRGG

Parental  DLMAYDRRGRPGDRYDGMVGFSADETW-DSAIDTWSPSEWQMAYEPQGGSGYDY
          DL..YD.RGRP.D.Y.GMVGF.ADETW.DSAI.TWSPS.WQ.AYEPQGGS.YDY
Retrocopy DLTTYDSRGRPEDCYNGMVGFTADETW<DSAIETWSPSQWQVAYEPQGGSIYDY

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	410.72 RPM
SRP012922_cerebellum	0.27 RPM	287.58 RPM
SRP012922_heart	0.00 RPM	109.98 RPM
SRP012922_kidney	0.00 RPM	225.61 RPM
SRP012922_liver	0.00 RPM	191.03 RPM
SRP012922_lung	0.00 RPM	315.53 RPM
SRP012922_quadricep_muscle	0.00 RPM	124.10 RPM
SRP012922_spleen	0.00 RPM	437.59 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_1433 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 15 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000026	4 retrocopies	retro_dnov_1433 , retro_dnov_1820, retro_dnov_2316, retro_dnov_2638,
Dasypus novemcinctus	ENSDNOG00000008688	6 retrocopies	retro_dnov_1146, retro_dnov_1399, retro_dnov_1672, retro_dnov_1823, retro_dnov_2434, retro_dnov_452,
Dipodomys ordii	ENSDORG00000016024	1 retrocopy	retro_dord_673,
Gorilla gorilla	ENSGGOG00000015500	2 retrocopies	retro_ggor_1764, retro_ggor_1866,
Loxodonta africana	ENSLAFG00000026567	1 retrocopy	retro_lafr_809,
Macaca mulatta	ENSMMUG00000018871	1 retrocopy	retro_mmul_2111,
Monodelphis domestica	ENSMODG00000008402	1 retrocopy	retro_mdom_1666,
Mus musculus	ENSMUSG00000021546	2 retrocopies	retro_mmus_1131, retro_mmus_2137,
Nomascus leucogenys	ENSNLEG00000003486	3 retrocopies	retro_nleu_1178, retro_nleu_1815, retro_nleu_973,
Otolemur garnettii	ENSOGAG00000007478	3 retrocopies	retro_ogar_2635, retro_ogar_2966, retro_ogar_3086,
Pongo abelii	ENSPPYG00000019327	3 retrocopies	retro_pabe_2105, retro_pabe_2106, retro_pabe_42,
Sarcophilus harrisii	ENSSHAG00000017109	1 retrocopy	retro_shar_820,
Tarsius syrichta	ENSTSYG00000001196	3 retrocopies	retro_tsyr_1664, retro_tsyr_1796, retro_tsyr_2149,
Tursiops truncatus	ENSTTRG00000004906	1 retrocopy	retro_ttru_1622,
Tursiops truncatus	ENSTTRG00000016693	7 retrocopies	retro_ttru_1144, retro_ttru_180, retro_ttru_1922, retro_ttru_444, retro_ttru_813, retro_ttru_930, retro_ttru_937,