RetrogeneDB ID: retro_dnov_2387

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_69916:3..538(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000012118
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000012037
• Aliases: None
• Description: None

Sequence

>retro_dnov_2387
CAGGAGTGGAAGGCAATGCACCAGAGACTATATAGCATAGATGGAGAAGTGTGGAGGAGAGCAGTGTGGGAGAAGAATTG
AAAAGGATTGACCAGTACTATCTGGGATACAGTCAAGGGCAACGAAGCTTCACAATGGGAATGAAAGCCTTTTGAGACAT
GGCCAATGAAGAATTCAGGCAGGTGATGAATGGCTTTCAAAACCAGCTCAACAGGAAAGAGGAAATATTCTATGACTTTC
CCTCTGAAGTCCTCAAGTCTGTGGATTGGAGGGAGAAAGGCTACATGACTCCTGTGAAGAATCAGGGTCAGTGTGATTCT
TGTTGGGTTTTTAGTGCAGTTGGCTCCCTCAAATGACAGGTGTTTCAGAAAACTGGCAGACTTGTTTCACTCAGTGAGCA
GAATCTGGTGGACTGCTCTCAGGCTGAGGGCAAAATGGCTGCAAAAGTGGCTTCATGGACAACGCTTTCCGGTAAGTCAA
GGACAACAAAGGCCTTGATTTAGAGGAATCCTATCCATACACTGGAAGGGCAATG

Alignment

ORF - retro_dnov_2387 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.72 %
• Parental protein coverage: 53.92 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QQWKATHQRLYGMNEEGWRRAVWEKN-MKRIERHNLAYNLGQQSFTMGMNAFGDMTNEEFRQVMNGYQKQ
          Q.WKA.HQRLY....E.WRRAVWEKN..KRI....L.Y..GQ.SFTMGM.AF.DM.NEEFRQVMNG.Q.Q
Retrocopy QEWKAMHQRLYSIDGEVWRRAVWEKN<LKRIDQYYLGYSQGQRSFTMGMKAF*DMANEEFRQVMNGFQNQ

Parental  LNRKGKVFFDFLSEVPKSVDWREKGYVTPVKNQGECGSCWAFSAVGALEGQMFRKTGKLISLSEQNLVDC
          LNRK...F.DF.SEV.KSVDWREKGY.TPVKNQG.C.SCW.FSAVG.L..Q.F.KTG.L.SLSEQNLVDC
Retrocopy LNRKEEIFYDFPSEVLKSVDWREKGYMTPVKNQGQCDSCWVFSAVGSLK*QVFQKTGRLVSLSEQNLVDC

Parental  SQAEG-NHGCNGGLMDNAFQYVQDNRGLDSEDSYPYVGRDM
          SQAEG...GC..G.MDNAF..V.DN.GLD.E.SYPY.GR.M
Retrocopy SQAEG<QNGCKSGFMDNAFR*VKDNKGLDLEESYPYTGRAM

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	31.50 RPM
SRP012922_cerebellum	0.00 RPM	16.22 RPM
SRP012922_heart	0.00 RPM	84.69 RPM
SRP012922_kidney	0.00 RPM	921.05 RPM
SRP012922_liver	0.00 RPM	457.14 RPM
SRP012922_lung	0.00 RPM	159.90 RPM
SRP012922_quadricep_muscle	0.00 RPM	58.85 RPM
SRP012922_spleen	0.00 RPM	97.64 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_2387 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 11 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007548	8 retrocopies	retro_chof_1227, retro_chof_1332, retro_chof_1345, retro_chof_141, retro_chof_1464, retro_chof_2392, retro_chof_383, retro_chof_424,
Dasypus novemcinctus	ENSDNOG00000012037	1 retrocopy	retro_dnov_2387 ,
Dasypus novemcinctus	ENSDNOG00000012612	1 retrocopy	retro_dnov_2521,
Macropus eugenii	ENSMEUG00000002168	2 retrocopies	retro_meug_1349, retro_meug_1567,
Macropus eugenii	ENSMEUG00000014293	1 retrocopy	retro_meug_1873,
Macropus eugenii	ENSMEUG00000016209	2 retrocopies	retro_meug_159, retro_meug_1727,
Monodelphis domestica	ENSMODG00000002844	1 retrocopy	retro_mdom_1101,
Otolemur garnettii	ENSOGAG00000001349	2 retrocopies	retro_ogar_1053, retro_ogar_1373,
Ochotona princeps	ENSOPRG00000001030	2 retrocopies	retro_opri_186, retro_opri_499,
Petromyzon marinus	ENSPMAG00000003453	1 retrocopy	retro_pmar_7,
Tupaia belangeri	ENSTBEG00000016406	1 retrocopy	retro_tbel_2841,