RetrogeneDB ID: retro_dnov_2638

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_93079:1298..2045(+)
• 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_2638
CTGCTGTTACCAACACTCACTGCAACCAGGCAGCTCCCACTCCAATCTGGTGCTATAGAATGCTTAAATTACCAACATTA
TAAAAGAAGCTTCTTTGATTGCAAGTTGAGACTTGATTGCAAGTTGAGTCTTGCAGTAGGAATTATTGGGGGACAAAGGT
GCTAAAATCAAAGAACTTCAAGAGAACAATAGTCAGGCAATAGCAAAGTTTTTCCAAGAATGCTGTCCTTGTTTTACCAG
CAGGGGCATTCTTAGTGGAGGAAAGCCTGATAGAGTTGTAAAGTGAGTAGAGATTATCCTTGATTTTATATCTGTCTCCC
ATCAAAGGGCGTGCACAGGCCTATGATCTCAATTTTCCTGATGAGACCTATCATTATGGTGGTTTTCAATGATGTTTGGT
GAGGACCCTGGATGTCCCTTGGGATTTCCCATGTGGGTAAAAGGTGGTTTTGACAGAATGCCTCCTGGTCTGGGCAGGCA
TCTAGTACCTCCACCTTGAAGAGATTATGATGACATGAGTTCTGGTGGAGGACCTCCTCCTGGATGAGGTGACTGGGGTG
GCAACAGAGCTCAGAATTTTCCTCTTCCACCACCACCACCACCTAGAAGAGAAGATCTAAAGGCTATGACCAAAGAGGAA
GACCTGGAGACTGTTAGGATGGCATGGTTTGTTTCAGTGTTGATGATATATGGGACTTTGCAATAGATATATGGAGCCCA
TCAGAACGGCAGATGGCTTATGAACCA

Alignment

ORF - retro_dnov_2638 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.79 %
• Parental protein coverage: 64.12 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LQLPSPTATSQLPLESDAVECLNYQHYKGSDFDCELRLLIHQSLAGGIIG-VKGAKIKELRE-NTQTTIK
          L.LP..TAT.QLPL.S.A.ECLNYQHYK.S................GIIG..KGAKIKEL.E.N.Q...K
Retrocopy LLLPTLTATRQLPLQSGAIECLNYQHYKRSFXXXXXXXXXXXXXXVGIIG>DKGAKIKELQENNSQAIAK

Parental  LFQECCPHSTDRVVLIGGKPDRVVECIKIILDLISES-PIK-GRAQPYDPNFYDETYDYGG-FTMMFDDR
          .FQECCP..T.R..L.GGKPDRVV....IILD.IS.S.P.K.GRAQ.YD.NF.DETY.YGG.F.MMF...
Retrocopy FFQECCPCFTSRGILSGGKPDRVVK*VEIILDFISVS<PSK<GRAQAYDLNFPDETYHYGG<FSMMFGED

Parental  RGRPVGFPMRGRGGFDRMPPGRGGRPMPPSRRDYDDMSPRRGPPPPPPGRGGRGGSRARNLPLPPPPPPR
          .G.P.GFPM...GGFDRMPPG.G....PP..RDYDDMS...GPPP...G.G..GG.RA.N.PLPPPPPPR
Retrocopy PGCPLGFPMWVKGGFDRMPPGLGRHLVPPP*RDYDDMSSGGGPPP---G*GDWGGNRAQNFPLPPPPPPR

Parental  GGDLMA-YDRRGRPGDRYDGMVGFSADETWDSAIDTWSPSEWQMAYEP
          ..DL.A.YD.RGRPGD..DGMV.FS.D..WD.AID.WSPSE.QMAYEP
Retrocopy REDLKA<YDQRGRPGDC*DGMVCFSVDDIWDFAIDIWSPSERQMAYEP

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	0.00 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_2638 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,