RetrogeneDB ID: retro_dnov_1507

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_22045:38144..38843(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CASP12
• Ensembl ID: ENSDNOG00000001797
• Aliases: None
• Description: caspase 12 (gene/pseudogene) [Source:HGNC Symbol;Acc:19004]

Sequence

>retro_dnov_1507
TGTTATCATAGAGGGAAGATAAAAGAGGCAAGAGATATATCCAGTGATGGAGATGGAAGGCTGAACAGGCCTGGCCCTCA
TCACTTGCAACAAAGAATTTGACTACCTTTCTAAATGATATGGGGCTGAAACTGATATTTTGGGAATGAAAGACCTTCTT
GAAATCCTTGGATACTCAGTGGTTATAAAAGAGAATCTTACAGCTCAGGAAATGGAAACTGAGGTAAGACAGTTTGCTGC
CTGCCCTGAGCACCAATTCTAAGACAGCAATTCCTGGTGTTTATGTCACATGGCATCCTCGATGGAATCTATAGAAGGAA
GCATAGAGATAAAGAGCCAGATATTCTGAATGATGATACCATCTTCTGAATTTTCAACAACTATAACTGCCAGAACTTTA
AAGACAAGCCCAAGATCATCATCATGCAGGCCTGCCAAGTCATAGATGCTGGGATTGTTTTGATGACTGACATGGGAAAA
GCCTCTTCAGCTACATGTAGCTAGCTCTTGCCTTGTTCCATGTCATATGATGCTATTACAAAGGCCCATGTGGAGAAGGA
CTTCATTGCTTTCAAATCTTCAACTCCATATAATATTTCTTGGAGAATTGACACAAATGGCTCTCTCTTTATTTTGTGAC
TTATTCACTACACCAAAGAGTACTCTTTGTGTTACCATTTGGAAGAAGTCTTTCAAAGG

Alignment

ORF - retro_dnov_1507 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.04 %
• Parental protein coverage: 75.65 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CFFKPPKHQSLNISSDGEGGPNSPG-LIICNKEFDYLSKRHGAEIDIFGMKDLLENLGYSVVVKENLTAQ
          C...........ISSDG.G..N.PG.LI.CNKEFDYLSK..GAE.DI.GMKDLLE.LGYSVV.KENLTAQ
Retrocopy CYHRGKIKEARDISSDGDGRLNRPG>LITCNKEFDYLSK*YGAETDILGMKDLLEILGYSVVIKENLTAQ

Parental  EMETELRQFAARPEHRFSDST-FLVFMSHGILDGICGRKHRDKEPDILNDDTIFRIFNNCNCQNLKDKPK
          EMETE.RQFAA.PEH.F.DS..FLVFMSHGILDGI..RKHRDKEPDILNDDTIF.IFNN.NCQN.KDKPK
Retrocopy EMETEVRQFAACPEHQF*DSN<FLVFMSHGILDGIYRRKHRDKEPDILNDDTIF*IFNNYNCQNFKDKPK

Parental  IIITQACRGKGAGIVWMADMGEDSAALCSQLTHCSMSYDAVTKAHVEKDFIAFKSSTPHNISWRLHTDGS
          III.QAC....AGIV.M.DMG..S.A.CS.L..CSMSYDA.TKAHVEKDFIAFKSSTP.NISWR..T.GS
Retrocopy IIIMQACQVIDAGIVLMTDMGKASSATCS*LLPCSMSYDAITKAHVEKDFIAFKSSTPYNISWRIDTNGS

Parental  LFISRLIHCFKEYSWCCHLEEVFRK
          LFI..LIH..KEYS.C.HLEEVF..
Retrocopy LFIL*LIHYTKEYSLCYHLEEVFQR

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	8.75 RPM
SRP012922_cerebellum	0.00 RPM	0.96 RPM
SRP012922_heart	0.00 RPM	7.19 RPM
SRP012922_kidney	0.00 RPM	0.00 RPM
SRP012922_liver	0.00 RPM	8.20 RPM
SRP012922_lung	0.00 RPM	64.91 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.35 RPM
SRP012922_spleen	0.00 RPM	34.80 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_1507 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
Dasypus novemcinctus	ENSDNOG00000001797	1 retrocopy	retro_dnov_1507 ,
Dasypus novemcinctus	ENSDNOG00000013931	1 retrocopy	retro_dnov_1013,