RetrogeneDB ID: retro_nleu_2660

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397390.1:710733..711197(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AKTIP
• Ensembl ID: ENSNLEG00000001106
• Aliases: None
• Description: None

Sequence

>retro_nleu_2660
CCGCAAAGCACTTTACCCAGCCTGGAGGCTCCACCTCTTGCCACAGCAGCACAGACAGCTAATGGCATACCCGCTTCTAG
AAGACCCTTCTACCTGGAGGATCTTCTTGTGGCATCTACCTCTGTCATGAAGCAGAAGTCATCTGGCACCTGTGTGCAGT
CACCTCATCGCTCTGCATTTGTGTAGGTTGGAGCAGTTTCATTCAGCCTGGACTTTATCAAGACTGTGCATTTAGGCCTA
CGGTTCATATCCCTGATAACTATCTGGGTGTTGCCTGTCTACACGTGGTATTTGACGTTCCTGCCTTTCACATTTTCATT
AATTCCATCTCTGTGAACTGGATGTGCAGAGAGATTTGCAAAGTGGAGGCGGAACCATAATTGCACTTGGGAAGTCTCAT
CAGTACAAAGAAACATTTCTTCAAGATTGATACAGCAAGCCCCCTAAACCCACAGGCTACAGTA

Alignment

ORF - retro_nleu_2660 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.55 %
• Parental protein coverage: 53.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PKNALPITKPTSPAPAAQSTNGTHASYGPFYLEYSLLAEFTLVVKQKLPGVYVQPSYRSALMWFGVI-FI
          P...LP.......A.AAQ..NG..AS..PFYLE..LL...T.V.KQK..G..VQ...RSA....G...FI
Retrocopy PQSTLPSLEAPPLATAAQTANGIPASRRPFYLE-DLLVASTSVMKQKSSGTCVQSPHRSAFV*VGAV<FI

Parental  RHGLYQDGVFKFTVYIPDNYPDGDCPRLVFDIPVFHPLVDPTS-GELDVKR-AFAKWRRNHNHIWQV-LM
          ..GLYQD..F..TV.IPDNY....C...VFD.P.FH......S..ELDV.R..FAKWRRNHN..W.V.L.
Retrocopy QPGLYQDCAFRPTVHIPDNYLGVACLHVVFDVPAFHIFINSIS<CELDVQR<RFAKWRRNHNCTWEV<LI

Parental  YARRVFYKIDTASPLNPEAAV
          .....F.KIDTASPLNP.A.V
Retrocopy STKKHFFKIDTASPLNPQATV

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_2660 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 20 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016345	1 retrocopy	retro_amel_392,
Canis familiaris	ENSCAFG00000009500	1 retrocopy	retro_cfam_1826,
Choloepus hoffmanni	ENSCHOG00000013690	2 retrocopies	retro_chof_2533, retro_chof_629,
Callithrix jacchus	ENSCJAG00000001498	1 retrocopy	retro_cjac_2895,
Cavia porcellus	ENSCPOG00000006523	1 retrocopy	retro_cpor_622,
Dasypus novemcinctus	ENSDNOG00000004906	4 retrocopies	retro_dnov_1376, retro_dnov_1776, retro_dnov_2080, retro_dnov_756,
Equus caballus	ENSECAG00000020381	1 retrocopy	retro_ecab_504,
Homo sapiens	ENSG00000166971	2 retrocopies	retro_hsap_1458, retro_hsap_3152,
Gorilla gorilla	ENSGGOG00000014821	1 retrocopy	retro_ggor_1122,
Microcebus murinus	ENSMICG00000010810	3 retrocopies	retro_mmur_124, retro_mmur_333, retro_mmur_985,
Microcebus murinus	ENSMICG00000016793	1 retrocopy	retro_mmur_1191,
Monodelphis domestica	ENSMODG00000025788	1 retrocopy	retro_mdom_1881,
Nomascus leucogenys	ENSNLEG00000001106	1 retrocopy	retro_nleu_2660 ,
Otolemur garnettii	ENSOGAG00000014495	1 retrocopy	retro_ogar_365,
Oryzias latipes	ENSORLG00000013747	1 retrocopy	retro_olat_30,
Pongo abelii	ENSPPYG00000007351	2 retrocopies	retro_pabe_1204, retro_pabe_1205,
Pan troglodytes	ENSPTRG00000008116	1 retrocopy	retro_ptro_2282,
Rattus norvegicus	ENSRNOG00000011956	1 retrocopy	retro_rnor_1611,
Tupaia belangeri	ENSTBEG00000017105	5 retrocopies	retro_tbel_1063, retro_tbel_2864, retro_tbel_3350, retro_tbel_4130, retro_tbel_853,
Tursiops truncatus	ENSTTRG00000012705	1 retrocopy	retro_ttru_348,