RetrogeneDB ID: retro_dnov_2552

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_85046:4784..5358(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSNK1G2
• Ensembl ID: ENSDNOG00000007923
• Aliases: None
• Description: casein kinase 1, gamma 2 [Source:HGNC Symbol;Acc:2455]

Sequence

>retro_dnov_2552
AAATGTCTCTACACCAATGAATATGTAGCAATCAAACTGGACCCAATAAAATCACATGCTCCACAGCTTCATTTAGAGTA
CAGGTTTTATAAACTGTTCAGAAGTGCAGGTGAATTTCTCTCACAGCTATAATACTTTAGACCTTAAGAGAAATACAATG
CAAGGGTACTGGAGCATCTTTGCCTTAACTTGAAGGACTTGTTTGATCTCTGTGACAGAACTTTTACTGTGAAGATGGTG
TTAATGATAGCCATTCAGTTGCTTTCTCAAATGGAATATGTGCACTTAAAGAATCTCATTTACCAAGATGTCAAACCAGA
GACCTTCCTGTTTGGCTGGGAAGACAATAAGAAAGAGCATGTTATACAAATTATAGACTTTAGACTAGCCAAGGAATACA
TTGACCCTAGAACTGAAAAAAACACATACCTTATATAGAACGCAAAAGTTTAAGTGGTACTGCAAGATATATATCAGCAT
GCATCTTGGCAAAGAGCAAAACTGATGGGATGATTTGGAAGCTCTTTGCCATATGTTCATGTATTTCTTTTGAGGCAGCC
TACTCTGGCAAGGC

Alignment

ORF - retro_dnov_2552 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.4 %
• Parental protein coverage: 57.19 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KNLYTNEYVAIKLEPIKSRAPQLHLEYRFYKQLNTA-EGVPQVFYFGPCGKYNAMVLELLGPSLEDLFDL
          K.LYTNEYVAIKL.PIKS.APQLHLEYRFYK....A.E...Q..YF.P..KYNA.VLE.L...L.DLFDL
Retrocopy KCLYTNEYVAIKLDPIKSHAPQLHLEYRFYKLFRSAGEFLSQL*YFRP*EKYNARVLEHLCLNLKDLFDL

Parental  CDRTFTLKTVLMIAIQLITRMEHVHTRSLIYRDVKPENFLVGRPGGRRQHTVHIIDFGLAKEYIDP-ETR
          CDRTFT.K.VLMIAIQL...ME.VH...LIY.DVKPE.FL.G.......H...IIDF.LAKEYIDP.E..
Retrocopy CDRTFTVKMVLMIAIQLLSQMEYVHLKNLIYQDVKPETFLFGWEDNKKEHVIQIIDFRLAKEYIDP>ELK

Parental  K-HIPYREHKSLTGTARYMSINTHLGKEQSRRDDLEALGHMFMYFLRGSLPWQG
          K.H..YR..K.......Y.S...HLGKEQ...DDLEAL.HMFMYF..GSL.WQG
Retrocopy KTHTLYRTQKFKWYCKIYISM--HLGKEQN*WDDLEALCHMFMYFF*GSLLWQG

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	39.09 RPM
SRP012922_cerebellum	0.00 RPM	62.55 RPM
SRP012922_heart	0.00 RPM	11.14 RPM
SRP012922_kidney	0.00 RPM	38.61 RPM
SRP012922_liver	0.00 RPM	38.86 RPM
SRP012922_lung	0.00 RPM	51.47 RPM
SRP012922_quadricep_muscle	0.00 RPM	18.69 RPM
SRP012922_spleen	0.00 RPM	55.51 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_2552 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	ENSDNOG00000007923	1 retrocopy	retro_dnov_2552 ,
Dasypus novemcinctus	ENSDNOG00000018857	1 retrocopy	retro_dnov_2386,
Macaca mulatta	ENSMMUG00000006620	1 retrocopy	retro_mmul_1195,