RetrogeneDB ID: retro_dnov_2313

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_63084:2640..3036(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMD
• Ensembl ID: ENSDNOG00000017248
• Aliases: None
• Description: monocyte to macrophage differentiation-associated [Source:HGNC Symbol;Acc:7153]

Sequence

>retro_dnov_2313
TTCGTTGCTGCTTCTTATGCGCCATGGTTAAATCTCCGTGAACTTGGACCCCTGGCATCTCATATGCGTTGGTTTATCTG
GCTCATGGCAGCTGGAGGAACCATTTATGTATTTCTCTACCATGAAAAGTATAAGGTAGTTGAGCTATTTTTCTATCTCA
CAATGGGATTTTCTTCAGCCTTGGTGGTGGCATCAATGAATAACACTGATGGACTTCAGGAACTTGCCTGTGGGGGTTTA
TTTTATTGCTTGGGAGTTGTGTTCTTCAAGAGCGATGGCATCATTCCATTCGCCCATGCCATCTGGCATCTCTTTGTGGC
CACAGCAGCTGCAGTGCATTACTACACCATTTGGAAATATCTTTACCGAAGTCCTACAGACTTTATGTGACATTTA

Alignment

ORF - retro_dnov_2313 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.7 %
• Parental protein coverage: 56.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FIAASYAPWLNLRELGPLASHMRWFIWLMAAGGTIYVFLYHEKYKVVELFFYLTMGFSPALVVTSMNNTD
          F.AASYAPWLNLRELGPLASHMRWFIWLMAAGGTIYVFLYHEKYKVVELFFYLTMGFS.ALVV.SMNNTD
Retrocopy FVAASYAPWLNLRELGPLASHMRWFIWLMAAGGTIYVFLYHEKYKVVELFFYLTMGFSSALVVASMNNTD

Parental  GLHELACGGLIYCLGVVFFKSDGIIPFAHAIWHLFVATAAAVHYYAIWKYLYRSPTDFMRHL
          GL.ELACGGL.YCLGVVFFKSDGIIPFAHAIWHLFVATAAAVHYY.IWKYLYRSPTDFM.HL
Retrocopy GLQELACGGLFYCLGVVFFKSDGIIPFAHAIWHLFVATAAAVHYYTIWKYLYRSPTDFM*HL

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	1.56 RPM
SRP012922_cerebellum	0.00 RPM	9.49 RPM
SRP012922_heart	0.00 RPM	1.62 RPM
SRP012922_kidney	0.00 RPM	0.00 RPM
SRP012922_liver	0.00 RPM	0.00 RPM
SRP012922_lung	0.00 RPM	14.36 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.87 RPM
SRP012922_spleen	0.00 RPM	6.52 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_2313 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000205	1 retrocopy	retro_btau_777,
Choloepus hoffmanni	ENSCHOG00000013437	1 retrocopy	retro_chof_1814,
Dasypus novemcinctus	ENSDNOG00000017248	1 retrocopy	retro_dnov_2313 ,
Macropus eugenii	ENSMEUG00000007054	1 retrocopy	retro_meug_714,
Myotis lucifugus	ENSMLUG00000012876	1 retrocopy	retro_mluc_289,
Monodelphis domestica	ENSMODG00000014847	5 retrocopies	retro_mdom_1029, retro_mdom_1569, retro_mdom_1591, retro_mdom_670, retro_mdom_951,
Oryctolagus cuniculus	ENSOCUG00000010549	1 retrocopy	retro_ocun_222,
Otolemur garnettii	ENSOGAG00000005902	2 retrocopies	retro_ogar_3070, retro_ogar_3071,
Procavia capensis	ENSPCAG00000004969	1 retrocopy	retro_pcap_231,
Ictidomys tridecemlineatus	ENSSTOG00000016227	1 retrocopy	retro_itri_913,
Tursiops truncatus	ENSTTRG00000007915	1 retrocopy	retro_ttru_469,