RetrogeneDB ID: retro_nleu_1224

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397285.1:20236120..20236548(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENSG00000145919
• Ensembl ID: ENSNLEG00000000476
• Aliases: None
• Description: None

Sequence

>retro_nleu_1224
GCTCTGCCTTCCGGTGACCCGGAGCTCATTGCTCTCATCCTGGAGCAGCTCAAGAGCCAGGCCTGTTTGGCAGCTTCTGT
CGATGCTGCCTGGCCCCTGTGGACACCAAGCCAGCTTACCAAAACCGGAGGCGGAAAGCTGAGCGTTCGGTGTCCACACA
TCTGGATGAGCAGGACTAGAATCTTATGATGCGCAAAAGCCTATTGCAAAATGGTCAGAGGCAGAGTGAGGTTCAGTCAG
GGACATTGGAAGCTGGAGAAGACAGGGTTATTTCTCAGGCAGAGGATCCAAAATTATACCACATCCTCAGGCCACCAATG
GAACAAGCAAATCAAGAGTTCCTGGGTGCCCAGAAGACAGCAACGGTGCCAGCGCCCCCTTTAGAGCCCGAAGACCAGGA
CCCTCCAGCTCCAGCCCAGGGCGGTTCT

Alignment

ORF - retro_nleu_1224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.36 %
• Parental protein coverage: 51.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLPPGDPQLIALIVEQLKSR-GLFDSFRRDCLADVDTKPAYQNLRQKVDNFVSTHLDKQEWNPTMNKNQL
          .LP.GDP.LIALI.EQLKS..GLF.SF.R.CLA.VDTKPAYQN.R.K....VSTHLD.Q..N..M.K..L
Retrocopy ALPSGDPELIALILEQLKSQ<GLFGSFCRCCLAPVDTKPAYQNRRRKAERSVSTHLDEQD*NLMMRKSLL

Parental  RNGLRQSVVQSGMLEAGVDRIISQVVDPKLNHIFRPQIERAIHEFLAAQKKAAVPAPPPEPEGQDPPAPS
          .NG.RQS.VQSG.LEAG.DR.ISQ..DPKL.HI.RP..E.A..EFL.AQK.A.VPAPP.EPE.QDPPAP.
Retrocopy QNGQRQSEVQSGTLEAGEDRVISQAEDPKLYHILRPPMEQANQEFLGAQKTATVPAPPLEPEDQDPPAPA

Parental  QDTS
          Q..S
Retrocopy QGGS

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_1224 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 18 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034598	1 retrocopy	retro_btau_663,
Canis familiaris	ENSCAFG00000016776	1 retrocopy	retro_cfam_1374,
Callithrix jacchus	ENSCJAG00000031971	4 retrocopies	retro_cjac_1154, retro_cjac_1515, retro_cjac_1536, retro_cjac_953,
Homo sapiens	ENSG00000145919	3 retrocopies	retro_hsap_102, retro_hsap_1867, retro_hsap_993,
Gorilla gorilla	ENSGGOG00000010925	2 retrocopies	retro_ggor_1365, retro_ggor_794,
Microcebus murinus	ENSMICG00000002626	1 retrocopy	retro_mmur_1126,
Macaca mulatta	ENSMMUG00000013793	2 retrocopies	retro_mmul_803, retro_mmul_869,
Mus musculus	ENSMUSG00000044502	1 retrocopy	retro_mmus_3661,
Nomascus leucogenys	ENSNLEG00000000476	1 retrocopy	retro_nleu_1224 ,
Oryctolagus cuniculus	ENSOCUG00000014283	1 retrocopy	retro_ocun_1071,
Otolemur garnettii	ENSOGAG00000001107	3 retrocopies	retro_ogar_1477, retro_ogar_2663, retro_ogar_3112,
Pongo abelii	ENSPPYG00000016057	2 retrocopies	retro_pabe_1567, retro_pabe_1587,
Pan troglodytes	ENSPTRG00000017544	2 retrocopies	retro_ptro_1282, retro_ptro_757,
Ictidomys tridecemlineatus	ENSSTOG00000013505	1 retrocopy	retro_itri_1164,
Tupaia belangeri	ENSTBEG00000014046	1 retrocopy	retro_tbel_3451,
Tarsius syrichta	ENSTSYG00000007617	1 retrocopy	retro_tsyr_818,
Tursiops truncatus	ENSTTRG00000000384	2 retrocopies	retro_ttru_1004, retro_ttru_457,
Vicugna pacos	ENSVPAG00000004260	1 retrocopy	retro_vpac_452,