RetrogeneDB ID: retro_nleu_2372

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397348.1:5434902..5435762(-)
• Located in intron of: ENSNLEG00000000586

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGK1
• Ensembl ID: ENSNLEG00000001423
• Aliases: None
• Description: None

Sequence

>retro_nleu_2372
AAGGGAAGGGAAAACTCTGGGAACAAGGTTAAAGTGAGCCCGCCAAAGTAGAAGCTTTCCGAGCTTCACTTTCCAAGCTA
GGGGATGTGTATGTCAATGATGCTTTTGGCACTGCTCACAGAGCCCACAGCTCCATGGTAGGAGTCAGTCTGCCACAGAA
GGCTGGTGGTTTTTTGATGAAGAAGGAGCTGAACTACTTTGCCAAGGTCTTGGAGAGCCCATAGCAACCCTTCCTGGCCA
TTCTTGGTGGAGCTAAAGTTGCAGACAAGATCCACCTGATCAATAATATGCTGGACAAAGTCAATGAGATGATTATTGGT
GGTGGAACGGCTTTTACCTTCCTTAAGGTGCTCAACAACATGGAGACTGGCACTTCTCTGTTTGATGAAGAGGGAGCCAA
GATTGTCAAAGACCAAATGTCCCAAGCTGAGAAGAATGGTGTGAAGATTACCTTGCCTATTGACTTTGTCACTGCTGACA
AATTTGATGAGAATGCCAAGACTGGCCAAGCCACTGTGGCTTCTGGCATACCTGCTGGCTGGATGGGCTTGGACTGTGGT
CCTGAAAGCAGCAAGAAGTATGCTGAGACTGTCACTTGGGCTAAGCAGATTGTGTGGAATGGTCCTGTGGGGGTATTTGA
ATGGGAAGCTTTTGCCTGGGGAACCAAAGCCCTCATGGATGAGGTGGTGAAAGCCACTTCTAGGGGCTGCATTACCATCG
TAGGTGGTGGAAACACTGACACTTGCTGTGCCAAATGGAACACAGAAGATAAAATCAGACATGTGAGCACTAGGGGTGGT
ACCAGTTTAGAGCTCCTGGAAGGTAAAGTCCTTCCTGGGGTGGATGCTTTCAGCAATATT

Alignment

ORF - retro_nleu_2372 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.85 %
• Parental protein coverage: 68.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KGKDASGNKVK-AEPAKIEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFSEEVDPLEFAK
          KG...SGNKVK..EPAK.EAFRASLSKLGDVYVNDAFGTAHRAHSSMVGV.LPQKAGGF........FAK
Retrocopy KGRENSGNKVK<SEPAKVEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVSLPQKAGGFLMKKELNYFAK

Parental  ALESPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDL
          .LESP..PFLAILGGAKVADKI.LINNMLDKVNEMIIGGG.AFTFLKVLNNME.GTSLFDEEGAKIVKD.
Retrocopy VLESP*QPFLAILGGAKVADKIHLINNMLDKVNEMIIGGGTAFTFLKVLNNMETGTSLFDEEGAKIVKDQ

Parental  MSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGP
          MS.AEKNGVKITLP.DFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAE.VT.AKQIVWNGP
Retrocopy MSQAEKNGVKITLPIDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAETVTWAKQIVWNGP

Parental  VGVFEWEAFARGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLP
          VGVFEWEAFA.GTKALMDEVVKATSRGCITI.GGG.T.TCCAKWNTEDK..HVST.GG.SLELLEGKVLP
Retrocopy VGVFEWEAFAWGTKALMDEVVKATSRGCITIVGGGNTDTCCAKWNTEDKIRHVSTRGGTSLELLEGKVLP

Parental  GVDALSNI
          GVDA.SNI
Retrocopy GVDAFSNI

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_2372 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 29 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017619	1 retrocopy	retro_amel_117,
Bos taurus	ENSBTAG00000000894	1 retrocopy	retro_btau_1021,
Canis familiaris	ENSCAFG00000017270	2 retrocopies	retro_cfam_1194, retro_cfam_510,
Callithrix jacchus	ENSCJAG00000021082	3 retrocopies	retro_cjac_1367, retro_cjac_137, retro_cjac_4171,
Cavia porcellus	ENSCPOG00000023785	1 retrocopy	retro_cpor_102,
Equus caballus	ENSECAG00000014984	1 retrocopy	retro_ecab_557,
Felis catus	ENSFCAG00000013209	2 retrocopies	retro_fcat_123, retro_fcat_316,
Homo sapiens	ENSG00000102144	2 retrocopies	retro_hsap_1966, retro_hsap_90,
Gorilla gorilla	ENSGGOG00000017111	3 retrocopies	retro_ggor_1429, retro_ggor_2420, retro_ggor_3026,
Loxodonta africana	ENSLAFG00000011954	1 retrocopy	retro_lafr_13,
Macropus eugenii	ENSMEUG00000004779	3 retrocopies	retro_meug_11, retro_meug_1649, retro_meug_400,
Myotis lucifugus	ENSMLUG00000017791	2 retrocopies	retro_mluc_1657, retro_mluc_2159,
Macaca mulatta	ENSMMUG00000012874	1 retrocopy	retro_mmul_144,
Monodelphis domestica	ENSMODG00000004055	2 retrocopies	retro_mdom_140, retro_mdom_170,
Mus musculus	ENSMUSG00000062070	2 retrocopies	retro_mmus_29, retro_mmus_9,
Nomascus leucogenys	ENSNLEG00000001423	3 retrocopies	retro_nleu_2372 , retro_nleu_2610, retro_nleu_79,
Oryctolagus cuniculus	ENSOCUG00000014726	1 retrocopy	retro_ocun_171,
Otolemur garnettii	ENSOGAG00000011104	1 retrocopy	retro_ogar_73,
Procavia capensis	ENSPCAG00000002117	1 retrocopy	retro_pcap_17,
Pongo abelii	ENSPPYG00000020496	3 retrocopies	retro_pabe_134, retro_pabe_1624, retro_pabe_3770,
Pan troglodytes	ENSPTRG00000022052	2 retrocopies	retro_ptro_2, retro_ptro_3229,
Rattus norvegicus	ENSRNOG00000002467	7 retrocopies	retro_rnor_1526, retro_rnor_1527, retro_rnor_2603, retro_rnor_3, retro_rnor_462, retro_rnor_590, retro_rnor_611,
Sorex araneus	ENSSARG00000003956	1 retrocopy	retro_sara_14,
Sarcophilus harrisii	ENSSHAG00000001853	1 retrocopy	retro_shar_11,
Sus scrofa	ENSSSCG00000012440	1 retrocopy	retro_sscr_933,
Ictidomys tridecemlineatus	ENSSTOG00000001972	1 retrocopy	retro_itri_65,
Tupaia belangeri	ENSTBEG00000010309	1 retrocopy	retro_tbel_35,
Tarsius syrichta	ENSTSYG00000007917	1 retrocopy	retro_tsyr_40,
Vicugna pacos	ENSVPAG00000001208	1 retrocopy	retro_vpac_21,