RetrogeneDB ID: retro_dnov_2045

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_44355:4574..4799(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPA3
• Ensembl ID: ENSDNOG00000011718
• Aliases: None
• Description: replication protein A3, 14kDa [Source:HGNC Symbol;Acc:10291]

Sequence

>retro_dnov_2045
ATGGTGAACGTGATGGAACTGCTGAAGTGGCGCATCAACACCAGCATGCTAGCTCAGTTCATCGACCGGCCTGTATGCTT
CGTAGGGAGACTGGAAAAGATTCATCCCACAGGGAAAATGTTTATTCTTTCAGATGGAGAAGGGAAAAATGGAACCATTG
AGTTGATGGAGCCACTTGATGAAGAAATCTCTGGAATTGTGGAAGTAGTTGACGAACAAGGCAAC

Alignment

ORF - retro_dnov_2045 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.33 %
• Parental protein coverage: 79.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVDVMELPKWRINASMLAQFIDRPVCFVGRLEKIHPTEKMFILSDGEGKNGTIELMEPLDEEISGIVEVV
          MV.VMEL.KWRIN.SMLAQFIDRPVCFVGRLEKIHPT.KMFILSDGEGKNGTIELMEPLDEEISGIVEVV
Retrocopy MVNVMELLKWRINTSMLAQFIDRPVCFVGRLEKIHPTGKMFILSDGEGKNGTIELMEPLDEEISGIVEVV

Parental  GRVTN
          ....N
Retrocopy DEQGN

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	2.33 RPM	7.58 RPM
SRP012922_cerebellum	2.06 RPM	8.66 RPM
SRP012922_heart	1.86 RPM	3.71 RPM
SRP012922_kidney	2.74 RPM	6.84 RPM
SRP012922_liver	0.93 RPM	3.87 RPM
SRP012922_lung	3.36 RPM	9.77 RPM
SRP012922_quadricep_muscle	1.73 RPM	4.67 RPM
SRP012922_spleen	3.43 RPM	12.25 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_2045 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 20 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016401	1 retrocopy	retro_amel_1031,
Callithrix jacchus	ENSCJAG00000000705	1 retrocopy	retro_cjac_3111,
Cavia porcellus	ENSCPOG00000011748	2 retrocopies	retro_cpor_855, retro_cpor_998,
Dasypus novemcinctus	ENSDNOG00000011718	3 retrocopies	retro_dnov_1044, retro_dnov_1824, retro_dnov_2045 ,
Equus caballus	ENSECAG00000007680	2 retrocopies	retro_ecab_212, retro_ecab_819,
Felis catus	ENSFCAG00000025369	1 retrocopy	retro_fcat_1287,
Homo sapiens	ENSG00000106399	2 retrocopies	retro_hsap_2179, retro_hsap_3473,
Gorilla gorilla	ENSGGOG00000022464	2 retrocopies	retro_ggor_1727, retro_ggor_2342,
Microcebus murinus	ENSMICG00000000741	1 retrocopy	retro_mmur_934,
Myotis lucifugus	ENSMLUG00000007421	1 retrocopy	retro_mluc_852,
Macaca mulatta	ENSMMUG00000000854	2 retrocopies	retro_mmul_131, retro_mmul_909,
Mus musculus	ENSMUSG00000012483	1 retrocopy	retro_mmus_413,
Nomascus leucogenys	ENSNLEG00000016151	2 retrocopies	retro_nleu_308, retro_nleu_340,
Oryctolagus cuniculus	ENSOCUG00000000467	1 retrocopy	retro_ocun_1097,
Otolemur garnettii	ENSOGAG00000001018	1 retrocopy	retro_ogar_113,
Pongo abelii	ENSPPYG00000017787	2 retrocopies	retro_pabe_2062, retro_pabe_2868,
Pan troglodytes	ENSPTRG00000018927	1 retrocopy	retro_ptro_2354,
Rattus norvegicus	ENSRNOG00000008309	2 retrocopies	retro_rnor_2803, retro_rnor_53,
Sus scrofa	ENSSSCG00000023886	1 retrocopy	retro_sscr_297,
Tupaia belangeri	ENSTBEG00000010930	6 retrocopies	retro_tbel_1347, retro_tbel_1876, retro_tbel_2736, retro_tbel_4029, retro_tbel_87, retro_tbel_917,