RetrogeneDB ID: retro_nleu_1543

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397298.1:8775771..8776124(-)
• Located in intron of: ENSNLEG00000003079

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRB3
• Ensembl ID: ENSNLEG00000015936
• Aliases: None
• Description: None

Sequence

>retro_nleu_1543
GGCCTGGGGCTGCTCCTGGTGCTGGGCCTGCCGCTGCTGTCATCCCCGGGAACGACCCCGGGCGCAAATATCAACCCCTT
CTGCAAATGAGAGTAGCATTGTTTTGCCTACACCCACCAGCTCCGGCTCCAATAGAGCCGTTTCAGGGGGGCCGTCACTG
CTATCATCTTGGTCCTCTGATTCCTGGCCCTCTTGTTCCTGGCGGTGGGGCTGGCACTATTGGTGCAGAAGCTTCAGGAG
ATGCGGCAGATGGAGGGCACCTACTGGCCCAGCAGCAAGGAGCAGTTCTCCTATGTAGCTGAGGCCTGGGCCCCTCATAC
TCCAATGAGACCGTGTGGGGCTGCCTGCACATC

Alignment

ORF - retro_nleu_1543 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.11 %
• Parental protein coverage: 96.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GLGLLLALGLPFLLARWGRAWG-QISTTSANENSTILPSSTSSSSDGNLP-QEAVTAIIVVFSILAALLL
          GLGLLL.LGLP.LL...G...G.QIST.SANE.S..LP..TSS.S........AVTAII.V...LA.L.L
Retrocopy GLGLLLVLGLP-LLSSPGTTPG>QISTPSANESSIVLPTPTSSGSNRAVS<RGAVTAIILVL*FLALLFL

Parental  AVGLALLVRKLREKRQTEGTYRPSSEEQFSHAAEARAPQD-SKETVRGCLPI
          AVGLALLV.KL.E.RQ.EGTY.PSS.EQFS..AEA.AP...S.ETV.GCL.I
Retrocopy AVGLALLVQKLQEMRQMEGTYWPSSKEQFSYVAEAWAPHT<SNETVWGCLHI

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_1543 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016567	1 retrocopy	retro_cjac_868,
Homo sapiens	ENSG00000130545	2 retrocopies	retro_hsap_2747, retro_hsap_3478,
Gorilla gorilla	ENSGGOG00000007070	2 retrocopies	retro_ggor_1910, retro_ggor_2345,
Macaca mulatta	ENSMMUG00000005599	1 retrocopy	retro_mmul_1434,
Nomascus leucogenys	ENSNLEG00000015936	1 retrocopy	retro_nleu_1543 ,
Pongo abelii	ENSPPYG00000009457	2 retrocopies	retro_pabe_2222, retro_pabe_2873,
Pan troglodytes	ENSPTRG00000010367	1 retrocopy	retro_ptro_2984,
Rattus norvegicus	ENSRNOG00000047322	1 retrocopy	retro_rnor_1506,
Ictidomys tridecemlineatus	ENSSTOG00000002396	1 retrocopy	retro_itri_781,