RetrogeneDB ID: retro_nleu_2458

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397358.1:6813728..6814174(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DSTN
• Ensembl ID: ENSNLEG00000009679
• Aliases: None
• Description: None

Sequence

>retro_nleu_2458
GCCTCAGGAGTGCAAGCTGCTGATGAAGTATGTCGCATTTTTTATGACATGAGAATTCGTAAATGCCCCACACCAGAAGA
AATCAAGAAAAGAAGAAAGGCTGTCATTTTTTTTTGTCTCAGTGCAGACAAAAGTGCATCATGTAGAAGGCAAAGAGATC
TTGGTTGGAGATGCTGGTATAACAGCCTTTCAAGCATTTTGTGGGAATGCTTCCTGAAAAAGATTGTCGCTATGCTTTGT
ATGATGCAAGCTTTGAAACAAAAGAATCCAGAAGAATTGATGTTTTCTTGTGGGCACCAGAACTAGCACCTCTGAAAAGT
AAAATGATCTATACAAGCTCCAAGGATGCAATCAAAAAGAAATTTCAAGGCATAAAACATGAATGGTAAACAAATGGACC
AGAAGATCTCAATCGGGCTTGTATTGCTGAAAAGTTAGGTGGATCC

Alignment

ORF - retro_nleu_2458 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.11 %
• Parental protein coverage: 93.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ASGVQVADEVCRIFYDMKVRKCSTPEEIKKRKKAV-IFCLSADK-KCII-VEEGKEILVGDVGVTITDPF
          ASGVQ.ADEVCRIFYDM..RKC.TPEEIKKR.KAV....LSADK.KCI..VE.GKEILVGD.G.T....F
Retrocopy ASGVQAADEVCRIFYDMRIRKCPTPEEIKKRRKAVXXXXLSADK<KCIM<VE-GKEILVGDAGIT---AF

Parental  KHFVG-MLPEKDCRYALYDASFETKESRKEELMFFLWAPELAPLKSKMIYASSKDAIKKKFQGIKHECQA
          ..F.G.MLPEKDCRYALYDASFETKESR......FLWAPELAPLKSKMIY.SSKDAIKKKFQGIKHE...
Retrocopy QAFCG>MLPEKDCRYALYDASFETKESRRIDV--FLWAPELAPLKSKMIYTSSKDAIKKKFQGIKHEW*T

Parental  NGPEDLNRACIAEKLGGS
          NGPEDLNRACIAEKLGGS
Retrocopy NGPEDLNRACIAEKLGGS

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_2458 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 21 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015434	1 retrocopy	retro_btau_880,
Choloepus hoffmanni	ENSCHOG00000003110	5 retrocopies	retro_chof_1308, retro_chof_1656, retro_chof_1758, retro_chof_2297, retro_chof_72,
Cavia porcellus	ENSCPOG00000005573	2 retrocopies	retro_cpor_700, retro_cpor_812,
Dasypus novemcinctus	ENSDNOG00000000934	1 retrocopy	retro_dnov_24,
Erinaceus europaeus	ENSEEUG00000011893	1 retrocopy	retro_eeur_529,
Homo sapiens	ENSG00000125868	1 retrocopy	retro_hsap_952,
Gorilla gorilla	ENSGGOG00000009007	1 retrocopy	retro_ggor_768,
Microcebus murinus	ENSMICG00000013687	1 retrocopy	retro_mmur_765,
Macaca mulatta	ENSMMUG00000013786	1 retrocopy	retro_mmul_782,
Mus musculus	ENSMUSG00000015932	1 retrocopy	retro_mmus_3314,
Nomascus leucogenys	ENSNLEG00000005852	5 retrocopies	retro_nleu_139, retro_nleu_1494, retro_nleu_1571, retro_nleu_1777, retro_nleu_636,
Nomascus leucogenys	ENSNLEG00000009679	1 retrocopy	retro_nleu_2458 ,
Oryctolagus cuniculus	ENSOCUG00000027456	1 retrocopy	retro_ocun_1891,
Ochotona princeps	ENSOPRG00000000976	2 retrocopies	retro_opri_1078, retro_opri_696,
Pongo abelii	ENSPPYG00000010727	1 retrocopy	retro_pabe_812,
Pan troglodytes	ENSPTRG00000013275	1 retrocopy	retro_ptro_659,
Pteropus vampyrus	ENSPVAG00000000420	1 retrocopy	retro_pvam_1275,
Rattus norvegicus	ENSRNOG00000005924	1 retrocopy	retro_rnor_1710,
Sus scrofa	ENSSSCG00000007085	1 retrocopy	retro_sscr_954,
Tupaia belangeri	ENSTBEG00000017634	8 retrocopies	retro_tbel_1206, retro_tbel_1977, retro_tbel_2425, retro_tbel_2880, retro_tbel_2881, retro_tbel_4020, retro_tbel_679, retro_tbel_851,
Tursiops truncatus	ENSTTRG00000007291	1 retrocopy	retro_ttru_1503,