RetrogeneDB ID: retro_dnov_2546

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_8459:71117..71747(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000025932
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CFDP1
• Ensembl ID: ENSDNOG00000013266
• Aliases: None
• Description: craniofacial development protein 1 [Source:HGNC Symbol;Acc:1873]

Sequence

>retro_dnov_2546
GAGGAATTCAGCTCGGAAGACTTCCCCACCTCAGAGGAGGAGGAGAACTACGTGCCCTCAGATGGAGAGTATAGTGCAGA
CAATGTAAATGAATTAGTGAAGGAAGATGAAGTGGATGGTAAAGAGTGGACACAGAAAACCAAAGGCATTAAAAAAAAAA
AGTTTCAGCGCATTCCATCCAGGAAGAGAAAAGAAGGTGGTCTCTCATAGAAGGTGAGGAAGAGGAGGATGCCAGTGTGG
AATCTGGAGGAAGTAGCAGGGAGGAAGAAGACTCAGCTGCAGAGCAAGATAAAGGCTTTGGGTCAGAAGATTCAAGAAAA
AAAGGAAGGATGAACTCTGGACCAGCTTCCTCAATAATGTGGAACCAAAATCGAAAGTGCCTCTGAGTACACAAGTTAAG
AGAGGAGAAGAGACTGAAGAGATGAGTTCAAGTAAATTGTTGGTCAGAGCAAAAGAGCTAGAGAAACCTAACGAAATAGA
AAAGGTTAAAATCACCAAGGTGTTTGATCTTGCTGATAATGAAGTCATGGTAACTAAAGAAGTGGATGCCGCCTTCAGAG
ACCAAATCCTTTTCAGGAAAATGAGAAGCTAATGTTTCTTGCAGCACTACCATCATCTCTGCAGGGGTCA

Alignment

ORF - retro_dnov_2546 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.56 %
• Parental protein coverage: 70.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EEFDSEDFSTSEEDEDYVPSGGEYSEDDVNELVKEDEVDGEEQTQKTKG-KKRKSQSIPSRKRKQGALS-
          EEF.SEDF.TSEE.E.YVPS.GEYS.D.VNELVKEDEVDG.E.TQKTKG......Q.IPSRKRK.G.LS.
Retrocopy EEFSSEDFPTSEEEENYVPSDGEYSADNVNELVKEDEVDGKEWTQKTKGIXXXXFQRIPSRKRKEGGLS<

Parental  LDDEEEEDASAESGGSSSEEEDTAAEQEKGFGSEDARKK-KEDELWASFLNDVGPKSKVPPSTQVKRGEE
          ...EEEEDAS.ESGGSS.EEED.AAEQ.KGFGSED.RKK...DELW.SFLN.V.PKSKVP.STQVKRGEE
Retrocopy IEGEEEEDASVESGGSSREEEDSAAEQDKGFGSEDSRKK<RKDELWTSFLNNVEPKSKVPLSTQVKRGEE

Parental  TEEMSSSKLLVKTEELEKPKEIEKVKITKVFDFAGEEVR-TKEVDATSRE-AKSFFRNEKERPQTNGPSA
          TEEMSSSKLLV...ELEKP.EIEKVKITKVFD.A..EV..TKEVDA..R.....F..NEK.......PS.
Retrocopy TEEMSSSKLLVRAKELEKPNEIEKVKITKVFDLADNEVMVTKEVDAAFRD<PNPFQENEKLMFLAALPSS

Parental  LSSA
          L...
Retrocopy LQGS

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	20.61 RPM
SRP012922_cerebellum	0.14 RPM	27.22 RPM
SRP012922_heart	0.00 RPM	11.37 RPM
SRP012922_kidney	0.00 RPM	20.26 RPM
SRP012922_liver	0.00 RPM	11.46 RPM
SRP012922_lung	0.00 RPM	20.16 RPM
SRP012922_quadricep_muscle	0.00 RPM	12.46 RPM
SRP012922_spleen	0.00 RPM	20.60 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_2546 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000000695	1 retrocopy	retro_cpor_465,
Dasypus novemcinctus	ENSDNOG00000013266	2 retrocopies	retro_dnov_2442, retro_dnov_2546 ,
Echinops telfairi	ENSETEG00000016429	1 retrocopy	retro_etel_1574,
Myotis lucifugus	ENSMLUG00000000890	1 retrocopy	retro_mluc_2525,
Rattus norvegicus	ENSRNOG00000019326	1 retrocopy	retro_rnor_2289,
Ictidomys tridecemlineatus	ENSSTOG00000004124	2 retrocopies	retro_itri_1117, retro_itri_1815,
Tupaia belangeri	ENSTBEG00000015362	2 retrocopies	retro_tbel_1305, retro_tbel_2189,
Tursiops truncatus	ENSTTRG00000001215	1 retrocopy	retro_ttru_1385,