RetrogeneDB ID: retro_nleu_2077

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397326.1:3939807..3940175(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM50B
• Ensembl ID: ENSNLEG00000003887
• Aliases: None
• Description: None

Sequence

>retro_nleu_2077
ATGGCAGTCTTCCTAGATAATTTTCATTGGCCAGAATGTGAATGTATTGACTGGAGTGAGAGAAGAAATGTTGTGGCATC
TGTTGTGACAGGTATATTGTTTTTTACAGGCTGGTGGATAATGACGCAGCTGTGGTGTATTGTAGGCCAGAACAGTTGAA
CCATGCCTTTCACACATGTGGTGTATTTCCCACATTGGCTTTCTTCATGCTAAATGCTGTATCCAATGCTCAGGTGAGAG
GTGATAGCTATGAAAGCGGCTGTTTAGGAAGAACAGGTCCTTGAGTTTGGCTTTTCGTTGGTTTCATGTTGATGTTTGGG
GTACTTACTGCTTCCATGTGGATTCTTTTTGGTGCATATGTTACCCAA

Alignment

ORF - retro_nleu_2077 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.6 %
• Parental protein coverage: 78.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGFLDNFRWPECECIDWSERRNAVASVVAGILFFTGWWIMI-DAAVVYPKPEQLNHAFHTCGVFSTLAF
          MA.FLDNF.WPECECIDWSERRN.VASVV.GILFFTG.W....DAAVVY..PEQLNHAFHTCGVF.TLAF
Retrocopy MAVFLDNFHWPECECIDWSERRNVVASVVTGILFFTG-WWIM<DAAVVYCRPEQLNHAFHTCGVFPTLAF

Parental  FMINAVSNAQVRGDSYESGCLGRTGARVWLFIGFMLMFGSLIASMWILFGAYVTQ
          FM.NAVSNAQVRGDSYESGCLGRTG..VWLF.GFMLMFG.L.ASMWILFGAYVTQ
Retrocopy FMLNAVSNAQVRGDSYESGCLGRTGP*VWLFVGFMLMFGVLTASMWILFGAYVTQ

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_2077 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003928	1 retrocopy	retro_chof_422,
Gorilla gorilla	ENSGGOG00000034844	1 retrocopy	retro_ggor_1487,
Myotis lucifugus	ENSMLUG00000012388	1 retrocopy	retro_mluc_970,
Nomascus leucogenys	ENSNLEG00000003887	1 retrocopy	retro_nleu_2077 ,
Pan troglodytes	ENSPTRG00000013869	1 retrocopy	retro_ptro_1379,
Ictidomys tridecemlineatus	ENSSTOG00000023740	1 retrocopy	retro_itri_678,