RetrogeneDB ID: retro_dnov_1005

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_133579:4530..5058(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SH3YL1
• Ensembl ID: ENSDNOG00000003742
• Aliases: None
• Description: SH3 domain containing, Ysc84-like 1 (S. cerevisiae) [Source:HGNC Symbol;Acc:29546]

Sequence

>retro_dnov_1005
CATGTGATTGTTAAAGCCAAAGGTCTTGCAATTTTATTTGTGATTAAAGTTGGATTTCCAGTAACTGCTAGAAGAGGCAG
TGGGATCCTATTAGCACATCTTCCTGATGGAAAATGGTCAACACCTTCAGTCATTGGGATAGCTGACTTGGTGGAGGATT
TGAAATTGGAATTGAGATATCAGATTTGGTAACAATTTTGAAGTATGACAGAGCAGTAGAAGCCTTTGTAAAAGGTAGTA
CTCTAACACTTGGAGGGAATTTTACTGTGGCAGTTGGGTCCTTGGGAAGGAATTTGGAAGGAAATGTAGCCTTAAGAAGC
TCTGCATATCTCTTTACATGTTGTTAATCAAGAGGACTCTGCTGGCATATCTTTAGAAGGTAGATGTTTGATTGAGAGGG
AGGAAGCTAATCAAAAATTTTATTGTCAAGATATTCTTGCTTAAGACATTTTATTAAGAGATATACCACAGTGTGCTCAA
GCAGATCTTTATGAAAATCTTGATTCCTTTACTGAAAAGTATGAAAAT

Alignment

ORF - retro_dnov_1005 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.57 %
• Parental protein coverage: 61.7 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HVIAKAKGLAILSVIKAGFLVTARGGSGIVLARLPDGKWSAPSAIGIAGL-GGGFEIGIEISDLVTILKY
          HVI.KAKGLAIL.VIK.GF.VTAR.GSGI.LA.LPDGKWS.PS.IGIA.L.GGGFEIGIEISDLVTILKY
Retrocopy HVIVKAKGLAILFVIKVGFPVTARRGSGILLAHLPDGKWSTPSVIGIADL<GGGFEIGIEISDLVTILKY

Parental  DRAVEAFVKGGTLTLGGNFTVAVGSLGRNLEGNVALRSSAYLFTCC-SRGL-AGISLEGRCLIEREEANQ
          DRAVEAFVKG.TLTLGGNFTVAVGSLGRNLEGNVALRSSAYLFTCC.SRGL.AGISLEGRCLIEREEANQ
Retrocopy DRAVEAFVKGSTLTLGGNFTVAVGSLGRNLEGNVALRSSAYLFTCC*SRGL>AGISLEGRCLIEREEANQ

Parental  KFYCQDILA-DILLRDIPQCAQADLYENLDSFTEKYEN
          KFYCQDILA.DILLRDIPQCAQADLYENLDSFTEKYEN
Retrocopy KFYCQDILA*DILLRDIPQCAQADLYENLDSFTEKYEN

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	9.33 RPM
SRP012922_cerebellum	0.00 RPM	1.79 RPM
SRP012922_heart	0.00 RPM	0.70 RPM
SRP012922_kidney	0.00 RPM	7.39 RPM
SRP012922_liver	0.00 RPM	3.56 RPM
SRP012922_lung	0.00 RPM	4.58 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.00 RPM
SRP012922_spleen	0.00 RPM	1.37 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_1005 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013307	1 retrocopy	retro_chof_2097,
Dasypus novemcinctus	ENSDNOG00000003742	1 retrocopy	retro_dnov_1005 ,