RetrogeneDB ID: retro_dnov_1997

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_41412:10086..10591(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HIBADH
• Ensembl ID: ENSDNOG00000008640
• Aliases: None
• Description: 3-hydroxyisobutyrate dehydrogenase [Source:HGNC Symbol;Acc:4907]

Sequence

>retro_dnov_1997
ATAGTATCTTCCCCAGCAGCTGTAGCTGAAAAAGCAGACAGAATTATTACAATGATGCCCACAAGTATCTATGCAATTGA
AGGGTATTCTGGAGCAAATGGTCTTCTAAGGAAATTGAAGAAAGGTTCATTACTAATAGATTCCAGTACGATTGACCCCA
TAGTTTCAAAAGAATTGGCCAAAGAATTTGAGAAAATGGGAACAGTTTTCATGGATGCCCCTGTTTCTGGTAGTGTGGGG
GCTGCTTGGCCTGGGAACCTCACATTACGGTGGGAGGAGTTGAAGAAGAACTTGCTGCTGCCCAACAGTTGCTGGGGTTC
TCCAATGTGGTGTATTGCGGAGGTGGTGGAGCTGGGCAGGCTGCTAAGATCTGCAATAACATGTTAGCTGTTAGTATGAT
TGGAACTGCTGAAGCCATGAATCTTGGAAAAAGGTTAGGGCTTGACCCAAAACTATTGGCTAAATCCTGAATATAAGCTC
AGGACGGTGCTGGTCAAGTGACACA

Alignment

ORF - retro_dnov_1997 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.48 %
• Parental protein coverage: 51.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VVSSPADVAEKADRIITMLPTSINAIEVYSGANGILRKVKKGSLLIDSSTIDPTVSKELAKEVEKMGAVF
          .VSSPA.VAEKADRIITM.PTSI.AIE.YSGANG.LRK.KKGSLLIDSSTIDP.VSKELAKE.EKMG.VF
Retrocopy IVSSPAAVAEKADRIITMMPTSIYAIEGYSGANGLLRKLKKGSLLIDSSTIDPIVSKELAKEFEKMGTVF

Parental  MDAPVSGGVGAARSGNLT-FMVGGVEEEFAAAQQLLGCMGSNVVYCGGVGTGQAAKICNNMLLAISMIGT
          MDAPVSG.VGAA..GNLT...VGGVEEE.AAAQQLLG...SNVVYCGG.G.GQAAKICNNM.LA.SMIGT
Retrocopy MDAPVSGSVGAAWPGNLT<ITVGGVEEELAAAQQLLGF--SNVVYCGGGGAGQAAKICNNM-LAVSMIGT

Parental  AEAMNLGIRLGLDPKLLAK-ILNMSSGRCWSSDT
          AEAMNLG.RLGLDPKLLAK.ILN.SSGRCWSSDT
Retrocopy AEAMNLGKRLGLDPKLLAK<ILNISSGRCWSSDT

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	16.36 RPM
SRP012922_heart	0.00 RPM	41.30 RPM
SRP012922_kidney	0.00 RPM	92.00 RPM
SRP012922_liver	0.00 RPM	13.16 RPM
SRP012922_lung	0.00 RPM	21.84 RPM
SRP012922_quadricep_muscle	0.00 RPM	51.06 RPM
SRP012922_spleen	0.00 RPM	22.55 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_1997 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005849	1 retrocopy	retro_amel_678,
Choloepus hoffmanni	ENSCHOG00000003153	1 retrocopy	retro_chof_1225,
Dasypus novemcinctus	ENSDNOG00000008640	2 retrocopies	retro_dnov_1465, retro_dnov_1997 ,
Microcebus murinus	ENSMICG00000000512	1 retrocopy	retro_mmur_1059,
Mus musculus	ENSMUSG00000029776	1 retrocopy	retro_mmus_2360,
Oryctolagus cuniculus	ENSOCUG00000010349	1 retrocopy	retro_ocun_1896,
Sus scrofa	ENSSSCG00000016695	1 retrocopy	retro_sscr_792,
Ictidomys tridecemlineatus	ENSSTOG00000004108	1 retrocopy	retro_itri_395,
Tarsius syrichta	ENSTSYG00000014191	1 retrocopy	retro_tsyr_1136,
Tursiops truncatus	ENSTTRG00000015276	4 retrocopies	retro_ttru_124, retro_ttru_150, retro_ttru_589, retro_ttru_807,
Vicugna pacos	ENSVPAG00000012531	1 retrocopy	retro_vpac_571,