RetrogeneDB ID: retro_nleu_2483

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397360.1:1312203..1312941(+)
• Located in intron of: ENSNLEG00000003492

Retrocopy information

• Ensembl ID: ENSNLEG00000003505
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_nleu_2483
TCCTTTGGGTGCCCTGAATATGGTCAGCTGGGACACAACTCAGATGGGAAGTTCATTGTCCCGGCATAGCGGATAGAGTA
TGACTGCGAACTAGTTCTCCCGCTAGTGGCCATCTTCATTGAGAAGACAAAAGATGGACAGATTCTTCCTGTACCAAACT
TGGTTATGCGAGGCGTGGCCTGTGGCGCTAACCACACGCTGGTCCTGGACTCCCAGAAGTGAGTCTTCTCCTGGGGCTTC
GGTGGCTATGGCTGGCTGGGCCACGCAGAGCAGAAGGATGAGATGGTCCCCTGCCTGGTGAAGCTGTTTGACTTCCCTGG
GCATGGGGCTTCCCAGATCTATGCTGGTTACACCTGCTTCTTTGCCGTCAGTGAAGTGGGTGGTCTGTTTTTCTGGGGGG
CCACCAACACCTCCCGTGAATCTACCATGTACCCAAAAGCAGTGCAGGACTTCTGCGGCTGGAGAATCCAGAGCCTGGCT
TGTGGGAAGAGCAGCAGCATTGTGGCCGCTGACGAGAGCACCATCAGCTGGGACCCATCACCGACCTTTGGGGAACTGGG
CTACAGGGACCACAAGCCCAAGTCTTCCACTACAGCCGAGGAGGTGAAGACTGTGCATGGCATTTTCTCAGAGCAGGTCG
CCATGGGCTACTCACACTCCTTGGTGATAGCAAGAGATGAAAGTGAGACTGAGAAAGAAAAGATCAAGAAACTGCCATAA
TACAGCCCCCGAACCCTC

Alignment

ORF - retro_nleu_2483 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.84 %
• Parental protein coverage: 57.61 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SFGCPEYGQLGHNSDGKFIARAQRIEYDCELVPRRVAIFIEKTKDGQILPVPNVVVRDVACGANHTLVLD
          SFGCPEYGQLGHNSDGKFI..A.RIEYDCELV...VAIFIEKTKDGQILPVPN.V.R.VACGANHTLVLD
Retrocopy SFGCPEYGQLGHNSDGKFIVPA*RIEYDCELVLPLVAIFIEKTKDGQILPVPNLVMRGVACGANHTLVLD

Parental  SQKRVFSWGFGGYGRLGHAEQKDEMVPRLVKLFDFPGRGASQIYAGYTCSFAVSEVGGLFFWGATNTSRE
          SQK.VFSWGFGGYG.LGHAEQKDEMVP.LVKLFDFPG.GASQIYAGYTC.FAVSEVGGLFFWGATNTSRE
Retrocopy SQK*VFSWGFGGYGWLGHAEQKDEMVPCLVKLFDFPGHGASQIYAGYTCFFAVSEVGGLFFWGATNTSRE

Parental  STMYPKAVQDLCGWRIRSLACGKSSIIVAADESTISWGPSPTFGELGYGDHKPKSSTAAQEVKTLDGIFS
          STMYPKAVQD.CGWRI.SLACGKSS.IVAADESTISW.PSPTFGELGY.DHKPKSST.A.EVKT..GIFS
Retrocopy STMYPKAVQDFCGWRIQSLACGKSSSIVAADESTISWDPSPTFGELGYRDHKPKSSTTAEEVKTVHGIFS

Parental  EQVAMGYSHSLVIARDESETEKEKIKKLPEYNPRTL
          EQVAMGYSHSLVIARDESETEKEKIKKLP.Y.PRTL
Retrocopy EQVAMGYSHSLVIARDESETEKEKIKKLP*YSPRTL

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_2483 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,