RetrogeneDB ID: retro_dnov_104

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_1605:406607..406950(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000007983
• Aliases: None
• Description: None

Sequence

>retro_dnov_104
ATGGTGCCACCCACGAGGGACTGCCTCCCCGGTGAACGTCTGTGTCATTTGGAGGAGGGCAGCCTGGGCAGAGGTACCTA
TGCCTGGCACAACGACATCTTCTCGTTACTTGCCCAGCTGCCTGATGAAAGCAGCAGAAACGGCGTGCTGCCTGCAGCGT
CTGGGATGGGAGAGACAGCCCCAGGTACTGCCAGCTCTGGGGGATATCGTAGCCAGGAAGGTCTCTAGCACCAATTCTCA
TTTTGCCAAAGTACATATCCTATAAGTTGGGTCCACACCACTTGAGAACTCCTTCTGAGGACCTATCCACATGGAAGGTA
CCCGAGCTACTGAAATAGACAAA

Alignment

ORF - retro_dnov_104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.48 %
• Parental protein coverage: 62.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAPPVRYCIPGERLCNLEEGSPGSGTYTRHGYIFSSLA-GCLTKSSENGALPVVSVMRETESQLLPDVGA
          M.PP.R.C.PGERLC.LEEGS.G.GTY..H..IFS.LA..CL.K..E..A........E...Q.LP..G.
Retrocopy MVPPTRDCLPGERLCHLEEGSLGRGTYAWHNDIFSLLA>SCLMKAAET-ACCLQRLGWERQPQVLPALGD

Parental  IVTCKVSSINSRFAKVHILYVGSTPLKNSFRGTIRKEDVRATEKDK
          IV..KVSS.NS.FAKVHIL.VGSTPL.NSF.G.I..E..RATE.DK
Retrocopy IVARKVSSTNSHFAKVHIL*VGSTPLENSF*GPIHMEGTRATEIDK

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	6.81 RPM
SRP012922_cerebellum	0.00 RPM	5.91 RPM
SRP012922_heart	0.00 RPM	3.25 RPM
SRP012922_kidney	0.00 RPM	4.93 RPM
SRP012922_liver	0.00 RPM	3.10 RPM
SRP012922_lung	0.00 RPM	7.48 RPM
SRP012922_quadricep_muscle	0.00 RPM	3.81 RPM
SRP012922_spleen	0.00 RPM	8.93 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_104 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006477	1 retrocopy	retro_chof_2075,
Dasypus novemcinctus	ENSDNOG00000007983	1 retrocopy	retro_dnov_104 ,
Erinaceus europaeus	ENSEEUG00000005647	3 retrocopies	retro_eeur_270, retro_eeur_438, retro_eeur_464,
Macropus eugenii	ENSMEUG00000002246	2 retrocopies	retro_meug_1799, retro_meug_951,
Myotis lucifugus	ENSMLUG00000009228	1 retrocopy	retro_mluc_1563,
Mus musculus	ENSMUSG00000034321	1 retrocopy	retro_mmus_691,
Oryctolagus cuniculus	ENSOCUG00000011898	1 retrocopy	retro_ocun_173,
Otolemur garnettii	ENSOGAG00000016259	1 retrocopy	retro_ogar_2496,
Pteropus vampyrus	ENSPVAG00000003372	1 retrocopy	retro_pvam_686,
Rattus norvegicus	ENSRNOG00000048708	1 retrocopy	retro_rnor_899,
Ictidomys tridecemlineatus	ENSSTOG00000006615	1 retrocopy	retro_itri_1253,