RetrogeneDB ID: retro_nleu_2176

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397333.1:12758240..12759269(+)
• Located in intron of: ENSNLEG00000003568

Retrocopy information

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

Parental gene information

• Parental gene symbol: OAT
• Ensembl ID: ENSNLEG00000000482
• Aliases: None
• Description: None

Sequence

>retro_nleu_2176
GTCCAAGGCCCTCCAACCTCTGATTACATTTTTGAAAGGGAATCTAAGTGTGGTGCGCACAATTACCATCCTTTACCTGT
AGCCCTGGAGAGAGGAAAATGTATTTACTTATGGGATGTAAAAGGCAGAAAATATTTTGACTTTCTGAGTTCTTACAGTG
CTGTCAACCAAGGGCATTGTCACCCCAAGATTGTGAATGCGCTAAAGAGTCAAGGGAACAAATTGACCTTAACTTCTAGA
GCTTTCTATAATAACGTACTTGGTGAATATGAGGAGTATATTACTAAACTTTTCAACTACCACAAAATTCTTCCTATGAA
TACAGGAATGGAAGCTGGAGAGACTGCCTGTAAACTAGCTCATAGGTGGGGCTATACCGTGAAGGGCATTCAGAAGTACA
AAGCAAAGGTTATTTTCGCAGCTGGAAACTTTTGGGGTAGGACGTTGTCTGCTATCTCCAGTTCCACAGACCTGACGAGT
TACGATGGTTTTGGACCGTTTATGCCGGGCTTCGACGTCATTCCCTGCAATGATCTGCCTGCACTGGAGCGTGCTTTTCA
GAATCCAAATGTAGCTGCATTCATGGTAGAACCAATTCAGGGTGAAGCAGGTGTTGTTCCAGATCCAGGTTACCTAATGG
GAGTGCGAGAGCTCCGCACCAGGCACCAGGATCTGTATATTGCTGACGAAATACAGTCAGGATTGGCCAGAACTGGTAGA
TGGCTGGCTGTTGATCATGCAAACGTCAGACCTGATATAGTCCTCCTTGGAAAGGCCCTTTCTGGGAGCTGATACTCTGT
GTCTGAAGTGCTGTGGGACGATGGCATAATGCTGAGCATTAAGCCAGGGGAACATGAGTCCACATACGGTGGCAATCCAC
TAGGCTGCCGAGTGGCCATCGCAGCCCTTGAGGTTTTAGAAGAAGAAAACCTTGCTGAAAATACAGAAAAAATGGGTATT
CTCTTGAGAAATGAACCCATGAAGCTACCTTCTGATGTTGTAACTGCCGTAAGAGGAAAATAATTACTT

Alignment

ORF - retro_nleu_2176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.37 %
• Parental protein coverage: 78.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VQGPPTSDDIFEREYKYGAHNYHPLPVALERGKGIYVWDVEGRKYFDFLSSYSAVNQGHCHPKIVNALKS
          VQGPPTSD.IFERE.K.GAHNYHPLPVALERGK.IY.WDV.GRKYFDFLSSYSAVNQGHCHPKIVNALKS
Retrocopy VQGPPTSDYIFERESKCGAHNYHPLPVALERGKCIYLWDVKGRKYFDFLSSYSAVNQGHCHPKIVNALKS

Parental  QVDKLTLTSRAFYNNVLGEYEEYITKLFNYHKVLPMNTGVEAGETACKLARKWGYTVKGIQKYKAKIVFA
          Q..KLTLTSRAFYNNVLGEYEEYITKLFNYHK.LPMNTG.EAGETACKLA..WGYTVKGIQKYKAK..FA
Retrocopy QGNKLTLTSRAFYNNVLGEYEEYITKLFNYHKILPMNTGMEAGETACKLAHRWGYTVKGIQKYKAKVIFA

Parental  AGNFWGRTLSAISSSTDPTSYDGFGPFMPGFDIIPYNDLPALERALQDPNVAAFMVEPIQGEAGVVVPDP
          AGNFWGRTLSAISSSTD.TSYDGFGPFMPGFD.IP.NDLPALERA.Q.PNVAAFMVEPIQGEAG.VVPDP
Retrocopy AGNFWGRTLSAISSSTDLTSYDGFGPFMPGFDVIPCNDLPALERAFQNPNVAAFMVEPIQGEAG-VVPDP

Parental  GYLMGVRELCTRHQVLFIADEIQTGLARTGRWLAVDYENVRPDIVLLGKALSGGLYPVSAVLCDDDIMLT
          GYLMGVREL.TRHQ.L.IADEIQ.GLARTGRWLAVD..NVRPDIVLLGKALSG..Y.VS.VL.DD.IML.
Retrocopy GYLMGVRELRTRHQDLYIADEIQSGLARTGRWLAVDHANVRPDIVLLGKALSGS*YSVSEVLWDDGIMLS

Parental  IKPGEHGSTYGGNPLACRVAIAALEVLEEENLAENAEKLGIILRNELMKLPSDVVTAVRGKGLL
          IKPGEH.STYGGNPL.CRVAIAALEVLEEENLAEN.EK.GI.LRNE.MKLPSDVVTAVRGK.LL
Retrocopy IKPGEHESTYGGNPLGCRVAIAALEVLEEENLAENTEKMGILLRNEPMKLPSDVVTAVRGK*LL

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_2176 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012633	1 retrocopy	retro_cjac_2462,
Homo sapiens	ENSG00000065154	1 retrocopy	retro_hsap_4828,
Gorilla gorilla	ENSGGOG00000000848	1 retrocopy	retro_ggor_3010,
Macropus eugenii	ENSMEUG00000005655	1 retrocopy	retro_meug_613,
Mus musculus	ENSMUSG00000030934	1 retrocopy	retro_mmus_3475,
Nomascus leucogenys	ENSNLEG00000000482	2 retrocopies	retro_nleu_2176 , retro_nleu_503,
Pongo abelii	ENSPPYG00000002737	2 retrocopies	retro_pabe_2989, retro_pabe_3754,
Pan troglodytes	ENSPTRG00000003028	1 retrocopy	retro_ptro_3213,
Sus scrofa	ENSSSCG00000010734	1 retrocopy	retro_sscr_1181,
Tursiops truncatus	ENSTTRG00000004225	1 retrocopy	retro_ttru_87,