RetrogeneDB ID: retro_nleu_1603

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397300.1:19137554..19138182(-)
• Located in intron of: ENSNLEG00000004883

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL8
• Ensembl ID: ENSNLEG00000010952
• Aliases: None
• Description: None

Sequence

>retro_nleu_1603
ATCATCCACAACCCGGGCCACAGCGTGCCCCTCCCCAAGGAGGTCTTCCGGGATCCGTACTGGTTTAAGAAGCGGATGGA
GCTTTTCATTGCTGCCGAGGGCATTCATACGGGCCAGTTTGTGTATTGCGGCAAGAAGGCCCAGCTCAACGTTGGCAGTG
TGCTCCCTGTGGGCACCGTGCCTGAGGGTATGATCGTGGGCTGCCTGGAGGAGAAACCTGGAGGCCGTAGCAAGCTGTCC
TGGGCATCAGGGAACTATGGCACTGCTATCTCCCACAACCCTGAGACCAAGAAGACCCGTGTGAAGCTGCCCTCTGGCTC
CAAGAAGGTTATCTCCTCAGCCAACAGAGCTGTGGTTGGTGTGGTGGCTGGAGGTGGCCGAACTGACAAACCCATCTTGA
AGGCTTGCCAAGCCTACCACAAATATAAGGCAAAGAGGAACTGGTGGCCACGAGTATGGGATGTGGCCATGAACCCTATG
GAGCATCCTTTTGGAGGTGCAACCACCAGCACGTCGGCATCCCCTCCACCATCTCAGAGATGACCCTGCTGGCTGCAAAA
TGGGTCTCATTGCTGCCTGCCAGATTGGACGTCTCTGGGGAACCAAGACTGTGCAGGAGAAAGAGAAC

Alignment

ORF - retro_nleu_1603 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.6 %
• Parental protein coverage: 81.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IIHDPGRGAPLAKVVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLE
          IIH.PG...PL.K.VFRDPY.FKKR.ELFIAAEGIHTGQFVYCGKKAQLN.G.VLPVGT.PEG.IV.CLE
Retrocopy IIHNPGHSVPLPKEVFRDPYWFKKRMELFIAAEGIHTGQFVYCGKKAQLNVGSVLPVGTVPEGMIVGCLE

Parental  EKPGDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILKAGRAYH
          EKPG.R.KL..ASGNY.T.ISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGR.DKPILKA..AYH
Retrocopy EKPGGRSKLSWASGNYGTAISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRTDKPILKACQAYH

Parental  KYKAKRNCWPRVRGVAMNPVEHPFGGG-NHQHIGKPSTIR-RDAPAGRKVGLIAARRTGRLRGTKTVQEK
          KYKAKRN.WPRV..VAMNP.EHPFGG..NHQH.G.PSTI..RD.PAG.K.GLIAA...GRL.GTKTVQEK
Retrocopy KYKAKRNWWPRVWDVAMNPMEHPFGGA<NHQHVGIPSTIS<RDDPAGCKMGLIAACQIGRLWGTKTVQEK

Parental  EN
          EN
Retrocopy EN

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_1603 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 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017933	1 retrocopy	retro_acar_31,
Bos taurus	ENSBTAG00000026327	1 retrocopy	retro_btau_96,
Canis familiaris	ENSCAFG00000001677	1 retrocopy	retro_cfam_1132,
Callithrix jacchus	ENSCJAG00000021388	4 retrocopies	retro_cjac_1109, retro_cjac_1169, retro_cjac_1579, retro_cjac_2047,
Cavia porcellus	ENSCPOG00000003854	2 retrocopies	retro_cpor_1006, retro_cpor_1415,
Dasypus novemcinctus	ENSDNOG00000009300	2 retrocopies	retro_dnov_2505, retro_dnov_503,
Macaca mulatta	ENSMMUG00000013379	2 retrocopies	retro_mmul_1470, retro_mmul_1531,
Mustela putorius furo	ENSMPUG00000006022	1 retrocopy	retro_mputfur_1517,
Nomascus leucogenys	ENSNLEG00000010952	2 retrocopies	retro_nleu_1603 , retro_nleu_594,
Oryctolagus cuniculus	ENSOCUG00000024716	1 retrocopy	retro_ocun_146,
Rattus norvegicus	ENSRNOG00000048523	2 retrocopies	retro_rnor_122, retro_rnor_239,