RetrogeneDB ID: retro_nleu_1737

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397306.1:16710557..16711280(-)
• Located in intron of: ENSNLEG00000006617

Retrocopy information

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

Parental gene information

• Parental gene symbol: THEM4
• Ensembl ID: ENSNLEG00000010322
• Aliases: None
• Description: None

Sequence

>retro_nleu_1737
ATGCTGAGGAGCTGCATCGGGCACCTCCGCACGCTGGGGGCCCTTTGCCGGCTGCCGCTGGTAGGCTGGCGCCTGCCGGG
TCGTGAGCCACGACCTGCGCTGAGGTCATTTTCTTCTGAGGATGTCATTCTTAAGGACTATTCTGTCCCCAACCCCAGCT
GGAACAAGGACCTAAGACTGCTCTTTGACCAGTTTATGAAGAAATGTGAAGATGACTCCTGGAAACATTTGCCTTCATAT
AAACGTACACGTACTGAAAGGATTCAAGACTTCAAAACCCGTTTTCTTGACCCAAAGCTTATGAAAGAAGAACAAGTGTC
ACAGGCCCAGCTCTTCACCAGAAGCTTTGATGATGGCCTGGGCTTTGAATACATGATGTTCTACAATGACGTTGAGAAAA
GGATGGTTTGCTTATTTCAAGGAGGCTCTTACCTGGAAGGACCACCTGGATTCATTCATGGAGGTGCCATTGCAACCATG
CTTGATGCTACTGTTGGTATGTGTGCAATGATGGCTGGGGGAATCGTCATGACTGCCAATCTCAACATCAATTGTAAAAG
ACCTATCCCTCTTTGTTCTGTTGTTATGATAAATAGCCAACTTGATAAAGTTGAAGGAAAGAAATTTTTTGTTTCCTGTA
ATGTTCAGAGTGTTGATGAGAAGACCCTATACTCAGAGATGACAAACTTATTTATAAAGCTGAATCCTGCTAAAAGTCTG
ACA

Alignment

ORF - retro_nleu_1737 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.04 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLRSCAACLRTPGAL-RRPPVGRRLPGSEPRPVLRSFSSEEVILKDCSVPNPSWNKDLRLLFDQFMKKCE
          MLRSC...LRT.GAL.R.P.VG.RLPG.EPRP.LRSFSSE.VILKD.SVPNPSWNKDLRLLFDQFMKKCE
Retrocopy MLRSCIGHLRTLGALCRLPLVGWRLPGREPRPALRSFSSEDVILKDYSVPNPSWNKDLRLLFDQFMKKCE

Parental  DGSWKRLPSYKRTPTERIQDFKTRFLDPKLMKEEQMSQAQLFTRSFDDGLGFEYVMFYNDVEKRMVCLFQ
          D.SWK.LPSYKRT.TERIQDFKTRFLDPKLMKEEQ.SQAQLFTRSFDDGLGFEY.MFYNDVEKRMVCLFQ
Retrocopy DDSWKHLPSYKRTRTERIQDFKTRFLDPKLMKEEQVSQAQLFTRSFDDGLGFEYMMFYNDVEKRMVCLFQ

Parental  GGPYLEGPPGFVHGGAIATMIDATVGMCAMMAGGIVMTANLNINYKRPIPLCSVVMINSQLDKVEGRKFF
          GG.YLEGPPGF.HGGAIATM.DATVGMCAMMAGGIVMTANLNIN.KRPIPLCSVVMINSQLDKVEG.KFF
Retrocopy GGSYLEGPPGFIHGGAIATMLDATVGMCAMMAGGIVMTANLNINCKRPIPLCSVVMINSQLDKVEGKKFF

Parental  VSCNVQSVDEKTLYSEATSLFIKLNPAKSLT
          VSCNVQSVDEKTLYSE.T.LFIKLNPAKSLT
Retrocopy VSCNVQSVDEKTLYSEMTNLFIKLNPAKSLT

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_1737 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 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000355	1 retrocopy	retro_amel_1301,
Choloepus hoffmanni	ENSCHOG00000000818	1 retrocopy	retro_chof_841,
Dasypus novemcinctus	ENSDNOG00000005970	1 retrocopy	retro_dnov_710,
Felis catus	ENSFCAG00000003443	1 retrocopy	retro_fcat_387,
Homo sapiens	ENSG00000159445	2 retrocopies	retro_hsap_1569, retro_hsap_978,
Gorilla gorilla	ENSGGOG00000008114	2 retrocopies	retro_ggor_1195, retro_ggor_782,
Microcebus murinus	ENSMICG00000010696	4 retrocopies	retro_mmur_1241, retro_mmur_1436, retro_mmur_1505, retro_mmur_1574,
Nomascus leucogenys	ENSNLEG00000010322	1 retrocopy	retro_nleu_1737 ,
Oryctolagus cuniculus	ENSOCUG00000005194	1 retrocopy	retro_ocun_1341,
Pongo abelii	ENSPPYG00000000851	1 retrocopy	retro_pabe_1295,
Pan troglodytes	ENSPTRG00000001301	2 retrocopies	retro_ptro_1056, retro_ptro_768,
Tupaia belangeri	ENSTBEG00000003352	2 retrocopies	retro_tbel_2412, retro_tbel_3266,
Tarsius syrichta	ENSTSYG00000005739	1 retrocopy	retro_tsyr_579,