RetrogeneDB ID: retro_dnov_1149

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_1549:52902..53235(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPAG7
• Ensembl ID: ENSDNOG00000011669
• Aliases: None
• Description: sperm associated antigen 7 [Source:HGNC Symbol;Acc:11216]

Sequence

>retro_dnov_1149
GTAGTGTTTCATAAAAGGATGGAAAAAGAGTGTCAGATTTCATCCAAGACAGTGGGCAGGTCAAGAAATGTTTCAGCAAT
GAGCAAGATAGAGAGGCACATACTACATCATATGGTGGAGTGGTTGGCCTGGCATCTTTCTCCTTCTGGGAAGATGACAA
GTGTCACTATATCATGATCTTCAAAAAGGAGTTTGCACTCTCAGATGAAGACCTGGACTCCTACTCATCATGGAGAGGAG
TGGAACTCAGATGGCTGAGGAAAAACAGAAGCTGAAGAGCTGGGCCCAGTGGCAGGAAGAGAGGCAGCCCAGTGGGGACG
TGCAGCTGTGAGC

Alignment

ORF - retro_dnov_1149 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.02 %
• Parental protein coverage: 57.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VEFRKRMEKE-VSDFIQDSGQTK-KKFQP-MSKIERSILHDVVE-VAGLTSFSFGEDDECRYVMIFKKEF
          V.F.KRMEKE.VSDFIQDSGQ.K...FQ..MSKIER.ILH..VE.V.GL.SFSF.EDD.C.Y.MIFKKEF
Retrocopy VVFHKRMEKE<VSDFIQDSGQVK<EMFQQ<MSKIERHILHHMVE<VVGLASFSFWEDDKCHYIMIFKKEF

Parental  APSDEELESY-RRGEEWDPQKAAEKRKLKELAQRQEEEAAQQGPTVVS
          A.SDE.L.SY...GEEW.......K....EL......EAAQ.G...VS
Retrocopy ALSDEDLDSY>HHGEEWN-SDG*GKTEAEELGPVAGREAAQWGRAAVS

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	41.42 RPM
SRP012922_cerebellum	0.00 RPM	73.27 RPM
SRP012922_heart	0.00 RPM	74.95 RPM
SRP012922_kidney	0.00 RPM	87.07 RPM
SRP012922_liver	0.00 RPM	25.85 RPM
SRP012922_lung	0.00 RPM	109.05 RPM
SRP012922_quadricep_muscle	0.00 RPM	92.43 RPM
SRP012922_spleen	0.00 RPM	77.83 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_1149 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006299	1 retrocopy	retro_amel_964,
Canis familiaris	ENSCAFG00000015761	1 retrocopy	retro_cfam_1417,
Dasypus novemcinctus	ENSDNOG00000011669	1 retrocopy	retro_dnov_1149 ,
Echinops telfairi	ENSETEG00000020098	1 retrocopy	retro_etel_1489,
Felis catus	ENSFCAG00000030469	1 retrocopy	retro_fcat_833,
Macropus eugenii	ENSMEUG00000007933	1 retrocopy	retro_meug_1358,
Myotis lucifugus	ENSMLUG00000014031	1 retrocopy	retro_mluc_1561,
Mus musculus	ENSMUSG00000018287	1 retrocopy	retro_mmus_2553,
Oryctolagus cuniculus	ENSOCUG00000001108	1 retrocopy	retro_ocun_1103,