RetrogeneDB ID: retro_dnov_2372

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_68320:45708..46325(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HAT1
• Ensembl ID: ENSDNOG00000011848
• Aliases: None
• Description: histone acetyltransferase 1 [Source:HGNC Symbol;Acc:4821]

Sequence

>retro_dnov_2372
ACGCTCTTTACAACCGTGGACTACACAACAGTCTATAATCACTACGTGTACCTAGACAAAACCTGGCCACGTGTAAGTCA
GATGCTGATACAGACTCATTTGAAGGTCAAGGCCATGGTGTTCAACTTCTGGAAACAGTGCATAGAAACAACATTGCATC
TCCTTCGGTTCTTGATAATACAGGGGAAGATCCATCCAAAAGCTTTGGGAAATTATGAGACTTTGTGCTTGTGAAGCTTT
GTCAAGATTTACCCTGTTTTTCCCAGGAAAAGTTAATGCAAGGATTCAATGACGATATGGCAACAGAGGCAAAATGCAAG
TTAAAAATAAATAAGGAACATGCTAGACGGGCTTATGAAATTCTTCAACTATTAGTAACTGACATGAGTGATGCTGAACA
GTACAGAAACTATAGATCGGATATTAAAAGAAGACTAATAAGTCCATATAAGAAAAAGCAGGGGGATCTTGCCAAGATGA
GAAAATGTCTCAGACCAGAAGAACTGACAAACCAGATGAACCAAATAGAAATAAGCATGCGGCATGAACAGCTGGAAGAA
AGCTTTCAGGAACTAATGGAAGACTACCAAAGTGTTATTGAACGACTTGCTCAAGAG

Alignment

ORF - retro_dnov_2372 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.57 %
• Parental protein coverage: 52.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TLFATVGYMTVYNYYVYPDKTRPRVSQMLILT-PFQGQGHGAQLLETVHRYYMASPSVLDITAEDPSKSY
          TLF.TV.Y.TVYN.YVY.DKT.PRVSQMLI.T..F.GQGHG.QLLETVHR...ASPSVLD.T.EDPSKS.
Retrocopy TLFTTVDYTTVYNHYVYLDKTWPRVSQMLIQT<SFEGQGHGVQLLETVHRNNIASPSVLDNTGEDPSKSF

Parental  VKLRDFVLVKLCQDLPCFSREKLMQGFNDDMAIEAQHKFKINKQHARRVYEILRLLVTDMSDAEQYRSYR
          .KL.DFVLVKLCQDLPCFS.EKLMQGFNDDMA.EA..K.KINK.HARR.YEIL.LLVTDMSDAEQYR.YR
Retrocopy GKL*DFVLVKLCQDLPCFSQEKLMQGFNDDMATEAKCKLKINKEHARRAYEILQLLVTDMSDAEQYRNYR

Parental  LDIKRRLISPYKKKQRDLAKMRKCLRPEELTNQMNQIEISMQHEQLEESFQELVEDYRRVIERLAQE
          .DIKRRLISPYKKKQ.DLAKMRKCLRPEELTNQMNQIEISM.HEQLEESFQEL.EDY..VIERLAQE
Retrocopy SDIKRRLISPYKKKQGDLAKMRKCLRPEELTNQMNQIEISMRHEQLEESFQELMEDYQSVIERLAQE

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	33.45 RPM
SRP012922_cerebellum	0.00 RPM	28.73 RPM
SRP012922_heart	0.00 RPM	22.97 RPM
SRP012922_kidney	0.00 RPM	23.82 RPM
SRP012922_liver	0.00 RPM	9.60 RPM
SRP012922_lung	0.00 RPM	37.88 RPM
SRP012922_quadricep_muscle	0.00 RPM	27.00 RPM
SRP012922_spleen	0.00 RPM	49.68 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_2372 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000011848	1 retrocopy	retro_dnov_2372 ,
Oryctolagus cuniculus	ENSOCUG00000005313	1 retrocopy	retro_ocun_1785,
Sorex araneus	ENSSARG00000005620	1 retrocopy	retro_sara_122,