RetrogeneDB ID: retro_dnov_838

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_113105:370..891(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ORC6
• Ensembl ID: ENSDNOG00000010859
• Aliases: None
• Description: origin recognition complex, subunit 6 [Source:HGNC Symbol;Acc:17151]

Sequence

>retro_dnov_838
AAAACAGAGGAGCACTCACGACTGTCCCAGGTGAGGTGTGCTGGCCTGTCTGCACATACCACAGCAAGCAGCAACGCAGC
CATGTGCCGGGACCTTGCCGCAGCCTTTATGACATGCCCCTTGGACAGGGCTGAGTTAATTAACCTTTCTGGTTTGAACA
AGAAGATGTATCCGTGCTACCTTAAATCTTTTGAGTGTTTACTGGCCTGAATTCAAACAGTGGAATAAGAGACCTAGCTG
TACAGTTTGGCTGTCCAGAAGCAGTGAACATGGCTTCAGAGATACTGGAAAGCTGTGAATCCTGTCTTCCACGGATACAG
AAAATAGACCTTGACTTCTCCAGGGCCCCTTTCACCACTGCTGCATTTCTTTCAGCATGCAAAGTTCTGAAGCTAAAAGT
GGATAAAAATAAAATGATAGACAAGTAATGTAAAAAAGGCATCTTTGATTGACTCTGTAAATAATTAGAGAAGATTGAAC
AGCAGATTGATGGAGAGCCTAGAGATTTAACTATTCCATCA

Alignment

ORF - retro_dnov_838 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.0 %
• Parental protein coverage: 69.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KAEEYFRLSQVKCSGLSAHTTETSNAVMCLNLAASFMTCPLDRVYFVRLSGLNKKMYQSCLKSFECLL-G
          K.EE..RLSQV.C.GLSAHTT..SNA.MC..LAA.FMTCPLDR.....LSGLNKKMY...LKSFECLL.G
Retrocopy KTEEHSRLSQVRCAGLSAHTTASSNAAMCRDLAAAFMTCPLDRAELINLSGLNKKMYPCYLKSFECLL<G

Parental  LKSN-GIRDLAVQFACTEAVNMASEILESYESGLPQTQKIDLDLSRPLFTTAALLSACKILKLKVDKNKM
          L.SN.GIRDLAVQF.C.EAVNMASEILES.ES.LP..QKIDLD.SR..FTTAA.LSACK.LKLKVDKNKM
Retrocopy LNSNSGIRDLAVQFGCPEAVNMASEILESCESCLPRIQKIDLDFSRAPFTTAAFLSACKVLKLKVDKNKM

Parental  VATSGVKKAIFDRLCKQLEKIGQQIDGEPRDLTTPS
          ......KK.IFD.LCK.LEKI.QQIDGEPRDLT.PS
Retrocopy I-DK*CKKGIFD*LCK*LEKIEQQIDGEPRDLTIPS

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	4.67 RPM
SRP012922_cerebellum	0.00 RPM	0.41 RPM
SRP012922_heart	0.00 RPM	0.46 RPM
SRP012922_kidney	0.00 RPM	0.27 RPM
SRP012922_liver	0.00 RPM	0.31 RPM
SRP012922_lung	0.00 RPM	1.83 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.00 RPM
SRP012922_spleen	0.00 RPM	14.88 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_838 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002944	1 retrocopy	retro_chof_2302,
Dasypus novemcinctus	ENSDNOG00000010859	1 retrocopy	retro_dnov_838 ,
Erinaceus europaeus	ENSEEUG00000012122	1 retrocopy	retro_eeur_489,
Otolemur garnettii	ENSOGAG00000000688	1 retrocopy	retro_ogar_1426,
Sarcophilus harrisii	ENSSHAG00000004207	2 retrocopies	retro_shar_211, retro_shar_759,
Tupaia belangeri	ENSTBEG00000000278	1 retrocopy	retro_tbel_3089,
Tarsius syrichta	ENSTSYG00000005205	2 retrocopies	retro_tsyr_1294, retro_tsyr_889,
Tursiops truncatus	ENSTTRG00000013294	1 retrocopy	retro_ttru_1528,