RetrogeneDB ID: retro_nleu_1306

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397288.1:25106409..25106796(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRTCAP2
• Ensembl ID: ENSNLEG00000011864
• Aliases: None
• Description: None

Sequence

>retro_nleu_1306
ACCTCACTGGCGATCTCCTCCCTCCTGTCCCTGCTGCTCTTCACTGGGATGCAGATGTAGATCCATCAGCTGGCCTCCAC
CGAGTGGCTTACCATCCAGGGTGGCCTGCATGGCTCAGGTCTCTTTGTGCTCTCCCTCACTGCCTTCAAGATTCTGGAGA
ATCTTGTGTTTGGCAAAGGATCCCAAGCAAAGACCTTCCCTGAGATTCTCCTGTGCCTCCTGTTGGCCCTCTTTGCGTCT
GGCCTCATCCACCGAGTCTGTGTCACCACCTGCTTCATATTCTCCATGGTTGGCCTGTGCTACATCAACAAGATCTCCAC
TCTGTATCAGGCAGCAGCTCCAGTCCTCACACCAGCCAAGGTCACAGGCAAGAGCAAGAAGAGAAAT

Alignment

ORF - retro_nleu_1306 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.23 %
• Parental protein coverage: 80.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TSLALSSLLSLLLFAGMQMYSRQLASTEWLTIQGGLLGSGLFVFSLTAFNNLENLVFGKGFQAKIFPEIL
          TSLA.SSLLSLLLF.GMQM...QLASTEWLTIQGGL.GSGLFV.SLTAF..LENLVFGKG.QAK.FPEIL
Retrocopy TSLAISSLLSLLLFTGMQM*IHQLASTEWLTIQGGLHGSGLFVLSLTAFKILENLVFGKGSQAKTFPEIL

Parental  LCLLLALFASGLIHRVCVTTCFIFSMVGLYYINKISSTLYQAAVPVLTPAKVTGKSKKRN
          LCLLLALFASGLIHRVCVTTCFIFSMVGL.YINKI.STLYQAA.PVLTPAKVTGKSKKRN
Retrocopy LCLLLALFASGLIHRVCVTTCFIFSMVGLCYINKI-STLYQAAAPVLTPAKVTGKSKKRN

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_1306 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 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011336	1 retrocopy	retro_amel_1789,
Canis familiaris	ENSCAFG00000017055	1 retrocopy	retro_cfam_1487,
Callithrix jacchus	ENSCJAG00000009017	1 retrocopy	retro_cjac_1289,
Felis catus	ENSFCAG00000025085	3 retrocopies	retro_fcat_1496, retro_fcat_477, retro_fcat_576,
Homo sapiens	ENSG00000163463	1 retrocopy	retro_hsap_2100,
Gorilla gorilla	ENSGGOG00000009303	1 retrocopy	retro_ggor_1635,
Macaca mulatta	ENSMMUG00000012180	2 retrocopies	retro_mmul_745, retro_mmul_987,
Mustela putorius furo	ENSMPUG00000005647	1 retrocopy	retro_mputfur_1653,
Nomascus leucogenys	ENSNLEG00000011864	1 retrocopy	retro_nleu_1306 ,
Oryctolagus cuniculus	ENSOCUG00000000347	1 retrocopy	retro_ocun_157,
Otolemur garnettii	ENSOGAG00000030271	1 retrocopy	retro_ogar_1306,
Pongo abelii	ENSPPYG00000000756	1 retrocopy	retro_pabe_1999,
Pan troglodytes	ENSPTRG00000001410	1 retrocopy	retro_ptro_1541,
Rattus norvegicus	ENSRNOG00000020542	1 retrocopy	retro_rnor_2128,
Ictidomys tridecemlineatus	ENSSTOG00000008829	1 retrocopy	retro_itri_1127,
Tarsius syrichta	ENSTSYG00000013228	2 retrocopies	retro_tsyr_1096, retro_tsyr_531,