RetrogeneDB ID: retro_dnov_1203

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_162302:700..993(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNAPC5
• Ensembl ID: ENSDNOG00000006689
• Aliases: None
• Description: small nuclear RNA activating complex, polypeptide 5, 19kDa [Source:HGNC Symbol;Acc:15484]

Sequence

>retro_dnov_1203
ATGCTGAGCCAGCTTCAGGAGCTGCACAAAGAGGAGGAAACACTGCTTCAGTTGAAGGCAGCACTGCATGATCAGCTGAA
CTGACTCAAGGTTGAAGAATTGACCCTTCAGTCAATGATTAGTTCTAGAAGAGGGATGAGATGCTTTCTTCTCAACCAGC
ACCTGAATCTTCACAAGATATGTTGATGCACGTAGACAATGAAGCATCAATCAACCAAACTGCACTGGAGTTGAGCAAAA
GAAGCCATGCTCTGGAAGAGGAGGTGGAGGAAGAGGAAGAAGAATCAGATTCC

Alignment

ORF - retro_dnov_1203 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.9 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLSRLQELRKEEETLLRLKAALHDQLNRLKVEELALQSMISSRRG-DEILSSQPAPESSQDILMHVDNEA
          MLS.LQEL.KEEETLL.LKAALHDQLN.LKVEEL.LQSMISSRRG.DE.LSSQPAPESSQD.LMHVDNEA
Retrocopy MLSQLQELHKEEETLLQLKAALHDQLN*LKVEELTLQSMISSRRG<DEMLSSQPAPESSQDMLMHVDNEA

Parental  SINQTALELSTRSHALEEEEEEEEEESDS
          SINQTALELS.RSHALEEE.EEEEEESDS
Retrocopy SINQTALELSKRSHALEEEVEEEEEESDS

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	8.95 RPM
SRP012922_cerebellum	0.00 RPM	7.01 RPM
SRP012922_heart	0.00 RPM	1.62 RPM
SRP012922_kidney	0.00 RPM	7.67 RPM
SRP012922_liver	0.00 RPM	3.56 RPM
SRP012922_lung	0.00 RPM	8.86 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.56 RPM
SRP012922_spleen	0.00 RPM	8.58 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_1203 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 12 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017304	1 retrocopy	retro_cfam_1063,
Callithrix jacchus	ENSCJAG00000007484	1 retrocopy	retro_cjac_2314,
Dasypus novemcinctus	ENSDNOG00000006689	1 retrocopy	retro_dnov_1203 ,
Gorilla gorilla	ENSGGOG00000003693	1 retrocopy	retro_ggor_2398,
Macropus eugenii	ENSMEUG00000003990	1 retrocopy	retro_meug_1590,
Macaca mulatta	ENSMMUG00000016841	1 retrocopy	retro_mmul_1815,
Mus musculus	ENSMUSG00000032398	1 retrocopy	retro_mmus_702,
Nomascus leucogenys	ENSNLEG00000012935	1 retrocopy	retro_nleu_2325,
Oryctolagus cuniculus	ENSOCUG00000008791	1 retrocopy	retro_ocun_1059,
Rattus norvegicus	ENSRNOG00000010156	1 retrocopy	retro_rnor_1087,
Ictidomys tridecemlineatus	ENSSTOG00000009201	1 retrocopy	retro_itri_1582,
Tupaia belangeri	ENSTBEG00000014333	1 retrocopy	retro_tbel_68,