RetrogeneDB ID: retro_nleu_1139

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397282.1:18419708..18420329(-)
• Located in intron of: ENSNLEG00000012263

Retrocopy information

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

Parental gene information

• Parental gene symbol: CD2BP2
• Ensembl ID: ENSNLEG00000015767
• Aliases: None
• Description: None

Sequence

>retro_nleu_1139
CAGGCCTCAGACTTGGAAGAGGAGGACAGCTTGGGCCAGACCCCAGTGAGTGCCCAAGCCCTCTTGGAGAGACTTTTGGA
GCTCCTATTGCCTAGAGAGACAGTGGCTAGGGCACTGAGGCATCTGGGGGCCCGAGGAGGAGGCAAAGGGAGCAGCAAAG
GGGCCTGGGTGACCCAGTTCCCTGCAGCGCCCAGAATGGCTCTCCGAATTGGCCAACTAGATGGTGGCCCGGGGAAACCT
TGGCATGCACCAGGAAACAATGGAACAGTTGGCCATGTGGCTGAAGGGTTTGGGGTACCAGGCCCTAGGGACCCCACAAT
CCCACACCCCCACAACTCCCTGGACATGTTCGCTGAGGAAGTGGCGGAGGGGGAACTGGAGACCCCAACCTCTACCCAGA
GAGGAGAAGCAGAGTTGCTGGGAGATGGTCTGGTGGATGTGATGTGGGAATATAAGTGGGAGAACCTGGGGGATGCCGAG
CTACATGGGCCCTTCACCAGCGCCCAGATGCAGACCTGGGTGAGCGAAGGCTACTTTCCTGATGGTGTTTATTGCCAGAA
GCTGGACCCCCTTGGTGGTCAGTTCTACAACTCCAAACGCATTGACTTTGACCTCTACACC

Alignment

ORF - retro_nleu_1139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.73 %
• Parental protein coverage: 60.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QASDSEEEDSLGQTPMSAQALLEGLLELLLPRETVAGALRRLGARGGG-KGS-KGPGRPSSPQRLDRLSG
          QASD.EEEDSLGQTP.SAQALLE.LLELLLPRETVA.ALR.LGARGGG.KG..KGPG.PSS.QR...LS.
Retrocopy QASDLEEEDSLGQTPVSAQALLERLLELLLPRETVARALRHLGARGGG>KGAAKGPG*PSSLQRPEWLSE

Parental  LADQMVARGNLGVYQETRERLAMRLKGLGCQTLG-PHNPTPPP-SLDMFAEEVAEEELETPTPTQRGEAE
          LA..MVARGNLG..QET.E.LAM.LKGLG.Q.LG.PHNPTPP..SLDMFAEEVAE.ELETPT.TQRGEAE
Retrocopy LAN*MVARGNLGMHQETMEQLAMWLKGLGYQALG>PHNPTPPQ>SLDMFAEEVAEGELETPTSTQRGEAE

Parental  SLGDGLVDVMWEYKWENTGDAELYGPFTSAQMQTWVSEGYFPDGVYCRKLDSAGGQFYNSKRIDFDLYT
          .LGDGLVDVMWEYKWEN.GDAEL.GPFTSAQMQTWVSEGYFPDGVYC.KLD..GGQFYNSKRIDFDLYT
Retrocopy LLGDGLVDVMWEYKWENLGDAELHGPFTSAQMQTWVSEGYFPDGVYCQKLDPLGGQFYNSKRIDFDLYT

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_1139 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
Homo sapiens	ENSG00000169217	1 retrocopy	retro_hsap_3900,
Gorilla gorilla	ENSGGOG00000014271	1 retrocopy	retro_ggor_2627,
Macaca mulatta	ENSMMUG00000021844	1 retrocopy	retro_mmul_1735,
Nomascus leucogenys	ENSNLEG00000015767	1 retrocopy	retro_nleu_1139 ,
Pongo abelii	ENSPPYG00000007267	1 retrocopy	retro_pabe_3179,
Pan troglodytes	ENSPTRG00000007995	1 retrocopy	retro_ptro_2653,