RetrogeneDB ID: retro_dnov_2692

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_99407:3815..4496(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RCC2
• Ensembl ID: ENSDNOG00000001396
• Aliases: None
• Description: regulator of chromosome condensation 2 [Source:HGNC Symbol;Acc:30297]

Sequence

>retro_dnov_2692
CGAAATGAGAAGGGACAGCTGGGACATGGTGACACCAAGAGAGTTGAGGCTCCCAGGCTCATCGAGGGTCTCAGCCACGA
GGCGATTGTGTCCGCGGCGTGTGGGCGGAACCACACCCTGGCCCTGACAGAAACGGGCTCTGTGTTTGCATTTGGCGAGA
ACAAGATGGGGCAGCTGGGCCTTGGCTACCAGACCGACGCGGTGCCCAGCCCGGCCCAGATAATGTACAACGGCCAGCCA
ATTACGAAAATGGCCTATGGGGCTGAATTCAGTATGATAATGGACTGTAAAGGAAACCTCTATTCCTTTGGGTGCCCTGA
ATATGGTCAGCTGGGACACAACTCTGATGGGAAGTTCATTGCACGAGCACAGCGGATAGAGTATGACTGCGAGCTGGTTC
CCCGGAGAGTGGCCATCTTCATCGAGAAGACGAAAGACGGGCAGATTTTGCCAGTACCGAATGTGGTTGTGCGAGATGTG
GCCTGTGGCGCCAACCACACGCTGGTCCTGGACTCCCAGAAGCGCGTCTTCTCCTGGGGGTTCGGTGGCTATGGGCGGCT
GGGCCACGCGGAGCAGAAGGACGAGATGGTGCTCTGCCTGGTGAAGCTGTTTGACTTCCCTGGTCGTGGGGCATCCCAGA
TCTATGCCGGCTACACCTGCTCCTTTGCCATCAGTGAAGTG

Alignment

ORF - retro_dnov_2692 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.63 %
• Parental protein coverage: 53.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RNEKGQLGHGDTKRVEAPRLIEGLSHEAIVSAACGRNHTLALTETGSVFAFGENKMGQLGLGNQTDAVPS
          RNEKGQLGHGDTKRVEAPRLIEGLSHEAIVSAACGRNHTLALTETGSVFAFGENKMGQLGLG.QTDAVPS
Retrocopy RNEKGQLGHGDTKRVEAPRLIEGLSHEAIVSAACGRNHTLALTETGSVFAFGENKMGQLGLGYQTDAVPS

Parental  PAQIMYNGQPITKMACGAEFSMIMDCKGNLYSFGCPEYGQLGHNSDGKFIARAQRIEYDCELVLRRVAIF
          PAQIMYNGQPITKMA.GAEFSMIMDCKGNLYSFGCPEYGQLGHNSDGKFIARAQRIEYDCELV.RRVAIF
Retrocopy PAQIMYNGQPITKMAYGAEFSMIMDCKGNLYSFGCPEYGQLGHNSDGKFIARAQRIEYDCELVPRRVAIF

Parental  IE-TKDGQILPVPNVXXXXXXXXXXXXLVLDSQKRVFSWGFGGYGRLGHAEQKDEMVPRLVKLFDFPGRG
          IE.TKDGQILPVPNV............LVLDSQKRVFSWGFGGYGRLGHAEQKDEMV..LVKLFDFPGRG
Retrocopy IEKTKDGQILPVPNVVVRDVACGANHTLVLDSQKRVFSWGFGGYGRLGHAEQKDEMVLCLVKLFDFPGRG

Parental  ASQIYAGYTCSFAVSEV
          ASQIYAGYTCSFA.SEV
Retrocopy ASQIYAGYTCSFAISEV

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	6.61 RPM	17.50 RPM
SRP012922_cerebellum	5.22 RPM	9.07 RPM
SRP012922_heart	0.93 RPM	4.64 RPM
SRP012922_kidney	3.29 RPM	7.39 RPM
SRP012922_liver	2.17 RPM	4.95 RPM
SRP012922_lung	4.28 RPM	14.97 RPM
SRP012922_quadricep_muscle	1.04 RPM	3.29 RPM
SRP012922_spleen	9.27 RPM	27.24 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_2692 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 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000001396	1 retrocopy	retro_dnov_2692 ,
Homo sapiens	ENSG00000179051	3 retrocopies	retro_hsap_2677, retro_hsap_3073, retro_hsap_3597,
Gorilla gorilla	ENSGGOG00000015263	1 retrocopy	retro_ggor_2112,
Nomascus leucogenys	ENSNLEG00000007783	2 retrocopies	retro_nleu_2483, retro_nleu_298,
Otolemur garnettii	ENSOGAG00000014544	1 retrocopy	retro_ogar_2967,
Pongo abelii	ENSPPYG00000025834	3 retrocopies	retro_pabe_2547, retro_pabe_2957, retro_pabe_748,
Pan troglodytes	ENSPTRG00000000247	3 retrocopies	retro_ptro_1804, retro_ptro_2072, retro_ptro_2434,
Rattus norvegicus	ENSRNOG00000006327	1 retrocopy	retro_rnor_1378,