RetrogeneDB ID: retro_nleu_298

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397263.1:1956953..1957678(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RCC2
• Ensembl ID: ENSNLEG00000007783
• Aliases: None
• Description: None

Sequence

>retro_nleu_298
AAACTTGAAGGGTCAAAGTGCAATGGGTAGTTTTGATTTTGGGGGCAACCAACTGGGACATGATTGGTCGAAAAGAAGTG
CCTAAACAGCAAGCTGCTTACCTCAATCTCGGTCAGAATTTGTGGGGTCCCCACAGGTATGGCTGTCTGGCGGGGGTCCG
GATACGGACTGTGGTCTCGGGTTCCTGTGCTGCACACAGCCTCCTCATCACCATGGAAGGGAAGCTGTGGGGTTGGGGTC
AAAACGAGAAGGGGCAGCTGGGACATGGCGACACCAAGAGAGTAGAGGCCCCCAGACTCATCGAGGGTCTCTGCCATGAA
GTGATCATGTCTGCAGCATGTGGGTGGAACCACACCTTGGCCTTGATGGAAACCGGCTCTGTGTTTGCGTTTGGGGAGAA
GAAGATGGGGCAGCTGGGCCTTGCCAACCAGACAGACGCTGTGCAGCCCCACGCAAATAATGTATAACGGCCAGCCAATT
ACCAAAATGGCCTGTGGGGCTGAATTCAGTATGATAATGACTGAAAAGGAAACCTCTATTCCTTTGGGTGCCCTGAGTAT
GGTCAGCTGGGACACAACTCGGGTGGGAAGTTCATCTTCGGCGCACAGCGGATAGAGTACGACTGCGAACTGGTCCCCCC
GCGACTGGCCATATTCATTGAGAAGATGAAAGACGGACAGATTCTGCCTGTACCAAACGTGGTTGTGGGAGACGTGGCCT
GTGGT

Alignment

ORF - retro_nleu_298 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 56.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KLEGSKCKG-QLLIFGATNWDLIGRKEVPKQQAAYRNLGQNLWGPHRYGCLAGVRVRTVVSGSCAAHSLL
          KLEGSKC.G...LI.GATNWD.IGRKEVPKQQAAY.NLGQNLWGPHRYGCLAGVR.RTVVSGSCAAHSLL
Retrocopy KLEGSKCNG<VVLILGATNWDMIGRKEVPKQQAAYLNLGQNLWGPHRYGCLAGVRIRTVVSGSCAAHSLL

Parental  ITTEGKLWSWGRNEKGQLGHGDTKRVEAPRLIEGLSHEVIVSAACGRNHTLALTETGSVFAF-GENKMGQ
          IT.EGKLW.WG.NEKGQLGHGDTKRVEAPRLIEGL.HEVI.SAACG.NHTLAL.ETGSVFAF.G....G.
Retrocopy ITMEGKLWGWGQNEKGQLGHGDTKRVEAPRLIEGLCHEVIMSAACGWNHTLALMETGSVFAF>GRRRWGS

Parental  LGLGNQTDAVPSPAQIMYNGQPITKMACGAEFSMIM-DCKGNLYSFGCPEYGQLGHNSDGKFIARAQRIE
          ..L........SP.QIMYNGQPITKMACGAEFSMIM.D.KGNLYSFGCPEYGQLGHNS.GKFI..AQRIE
Retrocopy WALPTR-QTLCSPTQIMYNGQPITKMACGAEFSMIM<D*KGNLYSFGCPEYGQLGHNSGGKFIFGAQRIE

Parental  YDCELVPRRVAIFIEKTKDGQILPVPNVVVRDVACG
          YDCELVP.R.AIFIEK.KDGQILPVPNVVV.DVACG
Retrocopy YDCELVPPRLAIFIEKMKDGQILPVPNVVVGDVACG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_298 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys 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,