RetrogeneDB ID: retro_dnov_345

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_3860:420040..420591(+)
• Located in intron of: ENSDNOG00000019824

Retrocopy information

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

Parental gene information

• Parental gene symbol: EPCAM
• Ensembl ID: ENSDNOG00000011799
• Aliases: None
• Description: epithelial cell adhesion molecule [Source:HGNC Symbol;Acc:11529]

Sequence

>retro_dnov_345
CTCTTTAAAGCCAGGTAGTACAAATTGCATCACCATGTGCTGTTGTGAGAACACTGCCAGGTCAGAAGAACAGATAAGAA
CACTGAAATAAAGTGTTCTGAACGTGTGAGGACCTACTGGATCTTCATGAAATTAAAACATAGAATAAGAGAAAAACCTG
AAGATGCTGGAAGCTTTCAGACTGCTCATGAGAAGGCAGTCACAATGCACTTGCAGCTGGATCTAAAATATGTCACAAAC
ATTCTATGTGAGAATTATGTTATCATCACTATTGATCTGGTGCAAAATTCTTCTCAGAAAACTCAAAATGATGTGGACAT
AGCTAACATGGCTTATTATTTTGAAAAAGATGTTAAGAGTAAATCCTTATTTCATTCCAATTGTGTGGACCTGAGAGTAA
ATGGGGAACAACCACATCTGGATCCTGGTCAAACTTTAATTTATTATGTTAATGAGCAATCACCTGAATTTTCATGCAGG
GTCTGAAAGCTGGTATTATTGCTGTAATTGTGGTTGTAACAATAGCAATTATTGCTGGAACTTTTGTACTG

Alignment

ORF - retro_dnov_345 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.8 %
• Parental protein coverage: 64.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LFKAR-QCNGTATCWCVNTAG-VRRTDKNTEITCSERVRTYWIIIELKHKTREKPYDVESLRYALETAIT
          LFKAR...N....C.C.NTA..VRRTDKNTEI.CSERVRTYWI...LKH..REKP.D..S...A.E.A.T
Retrocopy LFKAR>STNCITMCCCENTAR<VRRTDKNTEIKCSERVRTYWIFMKLKHRIREKPEDAGSFQTAHEKAVT

Parental  TRYQLDPKYITNILYENDV-ITIDLVQNSSQKTQNDVDIADVAYYFEKDVKGESLFHSNNMDLKVNGEQL
          ...QLD.KY.TNIL.EN.V.ITIDLVQNSSQKTQNDVDIA..AYYFEKDVK..SLFHSN..DL.VNGEQ.
Retrocopy MHLQLDLKYVTNILCENYVIITIDLVQNSSQKTQNDVDIANMAYYFEKDVKSKSLFHSNCVDLRVNGEQP

Parental  DLDPGQTLIYYVDEKSPEFS-MQGLQAGIIAVIVVVTIAIIAGIVVL
          .LDPGQTLIYYV.E.SPEFS.MQGL.AGIIAVIVVVTIAIIAG..VL
Retrocopy HLDPGQTLIYYVNEQSPEFS<MQGLKAGIIAVIVVVTIAIIAGTFVL

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	280.03 RPM
SRP012922_cerebellum	0.00 RPM	7.70 RPM
SRP012922_heart	0.00 RPM	0.93 RPM
SRP012922_kidney	0.00 RPM	64.62 RPM
SRP012922_liver	0.00 RPM	9.60 RPM
SRP012922_lung	0.00 RPM	49.02 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.00 RPM
SRP012922_spleen	0.00 RPM	1.26 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_345 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 17 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006474	1 retrocopy	retro_btau_66,
Choloepus hoffmanni	ENSCHOG00000013834	1 retrocopy	retro_chof_258,
Callithrix jacchus	ENSCJAG00000000624	1 retrocopy	retro_cjac_3006,
Dasypus novemcinctus	ENSDNOG00000011799	1 retrocopy	retro_dnov_345 ,
Erinaceus europaeus	ENSEEUG00000009462	1 retrocopy	retro_eeur_151,
Macropus eugenii	ENSMEUG00000015074	2 retrocopies	retro_meug_1984, retro_meug_474,
Microcebus murinus	ENSMICG00000000151	1 retrocopy	retro_mmur_739,
Macaca mulatta	ENSMMUG00000012390	1 retrocopy	retro_mmul_34,
Monodelphis domestica	ENSMODG00000001077	1 retrocopy	retro_mdom_104,
Mus musculus	ENSMUSG00000045394	1 retrocopy	retro_mmus_185,
Ochotona princeps	ENSOPRG00000004301	1 retrocopy	retro_opri_1225,
Pelodiscus sinensis	ENSPSIG00000015680	1 retrocopy	retro_psin_22,
Pan troglodytes	ENSPTRG00000011902	1 retrocopy	retro_ptro_92,
Rattus norvegicus	ENSRNOG00000015667	1 retrocopy	retro_rnor_252,
Sus scrofa	ENSSSCG00000008429	1 retrocopy	retro_sscr_69,
Ictidomys tridecemlineatus	ENSSTOG00000008631	1 retrocopy	retro_itri_106,
Tursiops truncatus	ENSTTRG00000004235	2 retrocopies	retro_ttru_21, retro_ttru_394,