RetrogeneDB ID: retro_dnov_515

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_5571:9349..9964(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KCTD10
• Ensembl ID: ENSDNOG00000007621
• Aliases: None
• Description: potassium channel tetramerization domain containing 10 [Source:HGNC Symbol;Acc:23236]

Sequence

>retro_dnov_515
AGCCAAATAAAATACTACCTGGTCCAGGGCCTACTGGAAGAATGCCAGGCGGCCCTACAAAACAAAGATACTTATGAGCC
TTTCTGAAAGTTCCTGTCATCACCTCTTCCAAGGAAGAACAAAACTTTCTAGTGACTTCAAATAAGCCAGCCGTGAAGGT
GCTCTACAATAGAAGTAACAACAGATACTCATATACCAGTAATTCTAACGACAACATGTGGAAAAACATTGAACTGTTTG
ATAAGCTGTCTCTGCACTTTAATGGAAGGGTCCTGTTCATAAAAGATGTCATTGGGGATGAGATCTGCTCCTGGTCCTTT
TATGGTCAGGGATGCAAGATTGCTGAAGTCTGTGGTACCTTCATCGTTTATGCCTCTGAGAAGAAACAGACCAAGGTAGA
GTTCCCTTCAGCCCGGATTTATGAAGAGACCCTAAACATCTTGCTGTATGAGGCCCAGGACAGCCAGGGACCTGACAATG
CACTCCTGGAGGCCACAGGCAGGGCAGCCGGGTGCTCGCAGCATCTGGACGAGGATGAGGAGCAGAAGGAGAGTGGATGG
AACGCGGGCGTCGATCCACCTCAAGCATCCAGACGACCGCGCCTATCTCCACCGG

Alignment

ORF - retro_dnov_515 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 65.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AEAKYYLVQGLVEECQAALQNKDTYEPF-CKVPVITSPKEEQKLIATSNKPAVKLLYNRSNNKYSYTSNS
          ...KYYLVQGL.EECQAALQNKDTYEPF..KVPVITS.KEEQ....TSNKPAVK.LYNRSNN.YSYTSNS
Retrocopy SQIKYYLVQGLLEECQAALQNKDTYEPF<LKVPVITSSKEEQNFLVTSNKPAVKVLYNRSNNRYSYTSNS

Parental  DDNMLKNIELFDKLSLRFNGRVLFIKDVIGDEICCWSFYGQGRKIAEVCCTSIVYATEKKQTKVEFPEAR
          .DNM.KNIELFDKLSL.FNGRVLFIKDVIGDEIC.WSFYGQG.KIAEVC.T.IVYA.EKKQTKVEFP.AR
Retrocopy NDNMWKNIELFDKLSLHFNGRVLFIKDVIGDEICSWSFYGQGCKIAEVCGTFIVYASEKKQTKVEFPSAR

Parental  IYEETLNILLYEAQDGRGPDNALLEATGGAAGRSHHLDEDEER-ERERIERVRR-IHIKRPDDRAHLHQ
          IYEETLNILLYEAQD..GPDNALLEATG.AAG.S.HLDEDEE..E.E..ER.RR.IH.K.PDDRA.LH.
Retrocopy IYEETLNILLYEAQDSQGPDNALLEATGRAAGCSQHLDEDEEQ<EGEWMERGRR<IHLKHPDDRAYLHR

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	0.19 RPM	69.43 RPM
SRP012922_cerebellum	0.00 RPM	6.74 RPM
SRP012922_heart	0.00 RPM	2.78 RPM
SRP012922_kidney	0.00 RPM	4.65 RPM
SRP012922_liver	0.00 RPM	3.56 RPM
SRP012922_lung	0.00 RPM	27.18 RPM
SRP012922_quadricep_muscle	0.00 RPM	2.77 RPM
SRP012922_spleen	0.00 RPM	27.93 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_515 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000007621	1 retrocopy	retro_dnov_515 ,
Dasypus novemcinctus	ENSDNOG00000010870	1 retrocopy	retro_dnov_1699,
Sus scrofa	ENSSSCG00000009934	1 retrocopy	retro_sscr_806,
Tursiops truncatus	ENSTTRG00000006406	1 retrocopy	retro_ttru_192,