RetrogeneDB ID: retro_nleu_1846

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397313.1:87519..87966(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THAP3
• Ensembl ID: ENSNLEG00000008620
• Aliases: None
• Description: None

Sequence

>retro_nleu_1846
CAGGTGAGGGAGAGCACAGACCCTGCCAGTGAGAGAGGAAACGCCAGCTCTTCTCAGGAAGAAAAGGTCCTCCCTGAGGC
GGGGGCTGGAGAGGACAGCCCTGGGAGAAACATGGACACTGCGGTTGAAGAGCTTCAGTTGCCCCCAAATGCCAAAGGCC
CCCTAAAACCGATCTCGCCACGGAGGCCGCAAGCAACAGAGGCTGTTGGCCGGCCGGCCCTGCAGGCTTGAGAAGGCCCC
CCGACAAGCAGCCATCTGATCACAGCTATGCCCTTTTGGACTTAGATTCCCTGAAGAAAAAAACTCTTCCTCACTCTGAA
GAAAAATGAAAAGCTCCAGAAGCGCTTGCAGGCCCAGAGGCTGGTGAAGTGAAGGATGTCCAGCCGCCTCCGTGCCTGAA
AAGGGCACCGGGGACTCGAGGCCAGACTTGGGCCAGAGCAGCAGAGC

Alignment

ORF - retro_nleu_1846 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.89 %
• Parental protein coverage: 62.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QVRENTDPASERGNASSSQKEKVLSEAGAREDSPGRNMDTALEELQLPPNAEGPVKQVSPRRPQATEAVG
          QVRE.TDPASERGNASSSQ.EKVL.EAGA.EDSPGRNMDTA.EELQLPPNA.GP.K..SPRRPQATEAVG
Retrocopy QVRESTDPASERGNASSSQEEKVLPEAGAGEDSPGRNMDTAVEELQLPPNAKGPLKPISPRRPQATEAVG

Parental  RPTGLAGLRRPP-NKQPSDHSYALLDLDSLK-KKLFLTLKENEKLRKRLQAQRLVMRRMCSRLRACKGHR
          RP..L.....PP..KQPSDHSYALLDLDSLK.KKLFLTLK.NEKL.KRLQAQRLV..RM.SRLRA.KGHR
Retrocopy RP-ALQA*EGPP<DKQPSDHSYALLDLDSLK>KKLFLTLKKNEKLQKRLQAQRLVK*RMSSRLRA*KGHR

Parental  GLQARLGPEQQS
          GL.ARLGPEQQS
Retrocopy GLEARLGPEQQS

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_1846 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000041988	1 retrocopy	retro_hsap_198,
Nomascus leucogenys	ENSNLEG00000008290	1 retrocopy	retro_nleu_2994,
Nomascus leucogenys	ENSNLEG00000008620	1 retrocopy	retro_nleu_1846 ,
Pongo abelii	ENSPPYG00000001935	1 retrocopy	retro_pabe_439,
Pan troglodytes	ENSPTRG00000000093	1 retrocopy	retro_ptro_179,