RetrogeneDB ID: retro_nleu_2225

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397335.1:4714629..4715127(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YY2
• Ensembl ID: ENSNLEG00000000999
• Aliases: None
• Description: None

Sequence

>retro_nleu_2225
AAAAAAGATACTGACTTTGGTACTTCAACAGTGGTTGAAGAACTGGCCATTGAAGAGAACCTGCCTCCTGATTTTCAGAG
TATATGACAGGAAAGAAACTTCCTCCTGGAGGAATGCCTGGCAGTAACCTCTCAAATCCTAAACAATGGGCATAACTTGC
TAGAATGAAGCCAAGAAAAATTAAGTAAGATGAAGCTCCAAGAACAACAGCTTGCCCTCATAAAGGGAGCACAAAAATGT
TCTTGGATAACTCTGCCATGAGAAAACACCTGCACAGCCACAGTCCCAGAGTCATCATCTGTGAAGAAATGGCAAAGCTC
TTGTTGAGAGCTCAAAACCAGAACGACACCAACCAGTCCGTGCTGGAGAGAAGCTCTTTCATGGCACACGGTAGGTCTGC
GGGAACGCTTTTTATTGGACTTCAATTTGCACACATGTGTGTGAATCCATACCAGAGACAGGACCCATGTGTGCTCCTTC
CGTGGTTGTAATAAAAGA

Alignment

ORF - retro_nleu_2225 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.24 %
• Parental protein coverage: 87.3 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KKDIDH--ETVVEEQIIGENSPPDY-SEYMTGKKLPPGGIPGIDLSDPKQLAEFARMKPRKIKEDDAPRT
          KKD.D....TVVEE..I.EN.PPD..SEYMTGKKLPPGG.PG..LS.PKQ.A..ARMKPRKIK.D.APRT
Retrocopy KKDTDFGTSTVVEELAIEENLPPDF<SEYMTGKKLPPGGMPGSNLSNPKQWA*LARMKPRKIK*DEAPRT

Parental  IACPHKGCTKMFRDNSAMRKHLHTHGPRVHVCAEC-GKAFVESSKLKRHQLVHTGEKPFQCTFEGCG-KR
          .ACPHKG.TKMF.DNSAMRKHLH.H.PRV..C.E..GKA.VESSK..RHQ.V..GEK.F..T...CG..R
Retrocopy TACPHKGSTKMFLDNSAMRKHLHSHSPRVIICEEM<GKALVESSKPERHQPVRAGEKLFHGTR*VCG<ER

Parental  FSLDFNLRTHVRIHTGDRPYVCPFDGCNKK
          F.LDFNL.T.V.IHT.DR..VC.F.GCNK.
Retrocopy FLLDFNLHTCV*IHTRDRTHVCSFRGCNKR

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_2225 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 10 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011146	1 retrocopy	retro_amel_2,
Callithrix jacchus	ENSCJAG00000016853	2 retrocopies	retro_cjac_1931, retro_cjac_4045,
Equus caballus	ENSECAG00000005805	1 retrocopy	retro_ecab_97,
Homo sapiens	ENSG00000100811	2 retrocopies	retro_hsap_106, retro_hsap_97,
Gorilla gorilla	ENSGGOG00000026332	2 retrocopies	retro_ggor_190, retro_ggor_2,
Mus musculus	ENSMUSG00000021264	1 retrocopy	retro_mmus_190,
Nomascus leucogenys	ENSNLEG00000000999	3 retrocopies	retro_nleu_1092, retro_nleu_116, retro_nleu_2225 ,
Otolemur garnettii	ENSOGAG00000006955	4 retrocopies	retro_ogar_1231, retro_ogar_1804, retro_ogar_1857, retro_ogar_289,
Pongo abelii	ENSPPYG00000025949	3 retrocopies	retro_pabe_145, retro_pabe_3616, retro_pabe_534,
Pan troglodytes	ENSPTRG00000006717	3 retrocopies	retro_ptro_3093, retro_ptro_45, retro_ptro_494,