RetrogeneDB ID: retro_nleu_3006

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397567.1:122409..123024(-)
• Located in intron of: ENSNLEG00000015609

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDCA8
• Ensembl ID: ENSNLEG00000011630
• Aliases: None
• Description: None

Sequence

>retro_nleu_3006
GTGGACAAGACCAACTCCTTAGGGAGGTGGAAGCTCGCTTCCTTTCTTAAAGACTTCGACTGCAAAGTGGAAATACGAAT
CAAGCCAATTGAGTCTGACAGGCAGAACCTCTTCAAGGAGGTGGATAACCTCTACAACATCCAGATCCTGGGGCTCCCCA
AGGCACTGCGCAAAGATGAATGGCTCAACTACTTCTCCCTTGGAGGAAACAAACAGGGCTTGGAAGAGGCAGCAACAGCT
GACCTGGATATCACCAAAATAAACAAACTAACCGCGGGAGCTATTCAAACACCCCTGAAATCTGCTGAAACACGAAAGGT
GATACAAGTAGATGAAATGATAGTGGAAGAGGAAGAAGAAGAAAATAAACATAAGAATCTTCAAACTGCAAGAGTCAAAA
GATGTCCTGCATCCAAGAAGAGAACTCAGTCTGTACAAGGAAAAGGCAGAAGGGAAAGGTCAAGCTGTGCTATCACTGTT
ACCCTAGTTTTGGGCCGACTGGACGTGTCCATAGTGAAGCCGACTCCAGGCCTGACACCCAGGTTTGACTCGAGGGTCTT
CATGATCCCTGGCCTGTGCACTCCTGCCACAGGAGAGCGGATTTCTAACAAAAGC

Alignment

ORF - retro_nleu_3006 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 73.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAKTNSLRRRKLASFLKDFDREVEIRIKQIESDRQNLLKEVDNLYNIEILRLPKALREMNWLDYFALGGN
          V.KTNSL.R.KLASFLKDFD..VEIRIK.IESDRQNL.KEVDNLYNI.IL.LPKALR...WL.YF.LGGN
Retrocopy VDKTNSLGRWKLASFLKDFDCKVEIRIKPIESDRQNLFKEVDNLYNIQILGLPKALRKDEWLNYFSLGGN

Parental  KQALEEAATADLDITEINKLTAEAIQTPLKSAKTRKVIQVDEMIVEEEEEEENEHKNLQTARVKRCPPSK
          KQ.LEEAATADLDIT.INKLTA.AIQTPLKSA.TRKVIQVDEMIVEEEEEE.N.HKNLQTARVKRCP.SK
Retrocopy KQGLEEAATADLDITKINKLTAGAIQTPLKSAETRKVIQVDEMIVEEEEEE-NKHKNLQTARVKRCPASK

Parental  KRTQSIQGRGKRKRSSRANTVTPAMGRLSVH-GQPTPGXXXRFSHSRVFKTPGLRTPAAGERIYNIS
          KRTQS.QG.G.R.RSS.A.TVT...GRL.V....PTPG...RF..SRVF..PGL.TPA.GERI.N.S
Retrocopy KRTQSVQGKGRRERSSCAITVTLVLGRLDVSIVKPTPGLTPRFD-SRVFMIPGLCTPATGERISNKS

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_3006 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 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000028556	2 retrocopies	retro_acar_139, retro_acar_200,
Choloepus hoffmanni	ENSCHOG00000004959	1 retrocopy	retro_chof_679,
Callithrix jacchus	ENSCJAG00000002008	1 retrocopy	retro_cjac_380,
Homo sapiens	ENSG00000134690	1 retrocopy	retro_hsap_4052,
Gorilla gorilla	ENSGGOG00000007719	2 retrocopies	retro_ggor_2594, retro_ggor_2721,
Microcebus murinus	ENSMICG00000011926	1 retrocopy	retro_mmur_1589,
Macaca mulatta	ENSMMUG00000014340	2 retrocopies	retro_mmul_1611, retro_mmul_2339,
Nomascus leucogenys	ENSNLEG00000011630	2 retrocopies	retro_nleu_2803, retro_nleu_3006 ,
Pongo abelii	ENSPPYG00000001526	2 retrocopies	retro_pabe_3224, retro_pabe_3234,
Pan troglodytes	ENSPTRG00000000552	3 retrocopies	retro_ptro_2531, retro_ptro_2533, retro_ptro_2746,