RetrogeneDB ID: retro_dnov_1840

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_32862:14916..15361(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CMBL
• Ensembl ID: ENSDNOG00000024697
• Aliases: None
• Description: carboxymethylenebutenolidase homolog (Pseudomonas) [Source:HGNC Symbol;Acc:25090]

Sequence

>retro_dnov_1840
GGGCAACAGCCATGGCACCCTTCTTATGACTCGTCCATCTTTCCCAAGTGGGTGAATATAAGAATTTCCAGGAAGATCAA
TAAAGATGTGGATGCTGTCTTTAAGTATTTGAAAGAACAGTGTCAGGCCCAGAAAACTGGTGTCATGGGATTCTGCTGGG
GTGGCATACTTGTCCATCATGTGATGATGAATAGTGGAAATTCAGGGCAAGAGTGTCTGTCTATGGCATTGTCAAGGATT
AAGAAGTCATATACAGTTTAAAGAATCCCACATTGTTTATTTTTGCTGAAAACAATTCTGTGATTTCTCTTGAGCAAGTC
TCTTCGCTGACCCAGAAGTTGAAAGAATACTGCAGAATTGAATGTCAAATTAAAACACTTTCTGTGCAAACCCATGAGTT
TGCGCTCAAAAGAGAGAAGCTTGTTCACCTGCAGACAAACTCTAT

Alignment

ORF - retro_dnov_1840 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.87 %
• Parental protein coverage: 86.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GQPPWHPSYDWAAFPEWVKTRNARTVDKEIDAVLKYLKQQCHAQKVGVVGFCWGGVAVHHVMTKYS-EFR
          GQ.PWHPSYD...FP.WV..R..R...K..DAV.KYLK.QC.AQK.GV.GFCWGG..VHHVM......FR
Retrocopy GQQPWHPSYDSSIFPKWVNIRISRKINKDVDAVFKYLKEQCQAQKTGVMGFCWGGILVHHVMMNSG<KFR

Parental  AGVSVYGIVKDFEDIYSLKNPTLFIFAENDAVISLEQVSLLTQKLKEHCKVEYQVKTFSGQTHGFV-HRK
          A.VSVYGIVKD.E.IYSLKNPTLFIFAEN..VISLEQVS.LTQKLKE.C..E.Q.KT.S.QTH.F....K
Retrocopy ARVSVYGIVKD*EVIYSLKNPTLFIFAENNSVISLEQVSSLTQKLKEYCRIECQIKTLSVQTHEFA<AQK

Parental  REDCSPADKPY
          RE.CSPADK.Y
Retrocopy REACSPADKLY

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	18.09 RPM
SRP012922_cerebellum	0.00 RPM	3.16 RPM
SRP012922_heart	0.00 RPM	13.23 RPM
SRP012922_kidney	0.00 RPM	141.28 RPM
SRP012922_liver	0.00 RPM	162.24 RPM
SRP012922_lung	0.00 RPM	8.09 RPM
SRP012922_quadricep_muscle	0.00 RPM	57.29 RPM
SRP012922_spleen	0.00 RPM	13.62 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_1840 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009759	1 retrocopy	retro_chof_2582,
Callithrix jacchus	ENSCJAG00000009079	1 retrocopy	retro_cjac_613,
Dasypus novemcinctus	ENSDNOG00000024697	2 retrocopies	retro_dnov_1840 , retro_dnov_2561,
Microcebus murinus	ENSMICG00000000533	1 retrocopy	retro_mmur_1038,
Otolemur garnettii	ENSOGAG00000016909	1 retrocopy	retro_ogar_2398,
Tupaia belangeri	ENSTBEG00000001698	1 retrocopy	retro_tbel_4449,