RetrogeneDB ID: retro_nleu_1005

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397278.1:3621527..3621983(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CASP3
• Ensembl ID: ENSNLEG00000010895
• Aliases: None
• Description: None

Sequence

>retro_nleu_1005
ATAATAATTAATGATAAGAATAAGTGGAATCATAAAAGCACTGGAATGGCATCTTGGTCTGGTACAGATGTCGGTGTGGC
AGACCTCAGGGAAACACTCACAAACTCGAAATATGAAGTCAGGAATCAAAATGATCTTACATGTCAAGAAATTGTGGAAT
TGATGCACACTTTTTCTTAAGAAGATCACAGCAAAAGGAGCAGTTTTGTTTGTGTGCTTCGGAGCCATGGTGAAGAAGGA
ATAATTTTTGGAACAAATGGACCCGTTGACCAGAAAAAGATAACAAGTTTTTTCAGAGGAGATTGTTGTAGAAGTCTAAC
TGGAAAACTCAAGCTTTTCATTATTCAGGCCTGCCGTGGTACAGAACTGGATTCTGACACTGAGACTGACACTGGTATTG
ATGATGACATGGCGTGTCATAAAATACCAGTGGAGGCCGAATTTTTGTATGCATAT

Alignment

ORF - retro_nleu_1005 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.26 %
• Parental protein coverage: 54.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IIINNKNF--HKSTGMASRSGTDVDAANLRETFRNLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFV
          IIIN.KN...HKSTGMAS.SGTDV..A.LRET..N.KYEVRN.NDLT..EIVELM...S.EDHSKRSSFV
Retrocopy IIINDKNKWNHKSTGMASWSGTDVGVADLRETLTNSKYEVRNQNDLTCQEIVELMHTFS*EDHSKRSSFV

Parental  CVLLSHGEEGIIFGTNGPVDLRKITNFFRGDRCRSLTGKPKLFIIQACRGTELDCGIETDSGVDDDMACH
          CVL.SHGEEGIIFGTNGPVD..KIT.FFRGD.CRSLTGK.KLFIIQACRGTELD...ETD.G.DDDMACH
Retrocopy CVLRSHGEEGIIFGTNGPVDQKKITSFFRGDCCRSLTGKLKLFIIQACRGTELDSDTETDTGIDDDMACH

Parental  KIPVEADFLYAY
          KIPVEA.FLYAY
Retrocopy KIPVEAEFLYAY

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_1005 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005740	2 retrocopies	retro_cjac_2678, retro_cjac_3011,
Dasypus novemcinctus	ENSDNOG00000013931	1 retrocopy	retro_dnov_1013,
Dipodomys ordii	ENSDORG00000002554	2 retrocopies	retro_dord_178, retro_dord_620,
Homo sapiens	ENSG00000164305	1 retrocopy	retro_hsap_406,
Gorilla gorilla	ENSGGOG00000025155	1 retrocopy	retro_ggor_402,
Macaca mulatta	ENSMMUG00000012053	1 retrocopy	retro_mmul_114,
Nomascus leucogenys	ENSNLEG00000010895	1 retrocopy	retro_nleu_1005 ,
Pongo abelii	ENSPPYG00000015236	1 retrocopy	retro_pabe_312,
Pan troglodytes	ENSPTRG00000016640	1 retrocopy	retro_ptro_310,
Rattus norvegicus	ENSRNOG00000010475	1 retrocopy	retro_rnor_2747,
Sarcophilus harrisii	ENSSHAG00000009178	1 retrocopy	retro_shar_404,
Ictidomys tridecemlineatus	ENSSTOG00000003865	2 retrocopies	retro_itri_172, retro_itri_586,