RetrogeneDB ID: retro_nleu_1811

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397311.1:7258494..7259264(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS18B
• Ensembl ID: ENSNLEG00000005224
• Aliases: None
• Description: None

Sequence

>retro_nleu_1811
ATGGTGATGCCCATATTAAACACCCTGCTGAGGCAGCTTCCTATCCTTTCTTTCTTCCGAAGTACCAATGGAGTTCAGGT
TCCCCTCCATACTCTTTCAGCAAAGCTCCTGAGAAAGAGTATTTGCCCCCAGTTCCCATTTCACTATATAAGAATGAACC
CTGGAAATATCTGGAATCAGAAGAATACCAGGAACCATAGGGTTCTCATCCCAACTGGGTGGACTATTGCCACTACTACA
AGGGTGGTATACCCCTGCAGCAGACTCAAAAGACATGTATACATAGGAATAAAGTTGCTGGGAATCCCTGCCGCATCTGC
CAACATCACAAGTTGCATGTTGACTTTAGGAATGTTAAGCTCTTGGAACAGTTTGTCAGTGCCCACATGGGTATTATCTT
CCATGCTCCATACACAGGAGTCTGTATGACGCAGCACAAGATGTTGATTCATGCCATCCAGAAAGCCAGGGATCATGGTC
TCCTCAGTTACCACATCCCCAAGTTGAACCCCAGGACCTTGATTTTAATGCCTCTCATGGAGTTATGAGTACTTCTCTGC
CAGTCCCCACCCTGGTCTCAGGTGAATCCTGGTACCTATGGTACAGCTGGAAACAGCCATCAGAGAGAGAACTGTCTCAC
CTTTGCCAACTCTATCAGGGTTATCGCTAAGAAGAGAGTGGCCCCCACATCTGAGTCAGTGCCCAAGATGCTCCCCACAA
CACCAGTGGAAGCCTCCTTCACTGAAGAGACAGGCCCCTAGAGTGCTCTG

Alignment

ORF - retro_nleu_1811 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAASVLNTLLRRLPMLSLFRGTHRVQVPLQTLC-TKAPSEEDSLSPVPISPYKDEPWKYLESEEYQERYG
          M....LNTLLR.LP.LS.FR.T..VQVPL.TL...KAP.E...L.PVPIS.YK.EPWKYLESEEYQE..G
Retrocopy MVMPILNTLLRQLPILSFFRSTNGVQVPLHTLS<SKAP-EKEYLPPVPISLYKNEPWKYLESEEYQEP*G

Parental  SRPVWADYRRNHKGGVPPQRTRKTCIRRNKVAGNPCPICRDHKLHVDFRNVKLLEQFVCAHTGIIFHAPY
          S.P.W.DY....KGG.P.Q.T.KTCI.RNKVAGNPC.IC..HKLHVDFRNVKLLEQFV.AH.GIIFHAPY
Retrocopy SHPNWVDYCHYYKGGIPLQQTQKTCIHRNKVAGNPCRICQHHKLHVDFRNVKLLEQFVSAHMGIIFHAPY

Parental  TGVCVKQHKRLTQAIQKARDHGLLIYHI-PQVEPRDLDFSTSHGAVSATPPAPTLISGDPWYPWYNWKQP
          TGVC..QHK.L..AIQKARDHGLL.YHI.PQVEP.DLDF..SHG..S...P.PTL.SG..WY.WY.WKQP
Retrocopy TGVCMTQHKMLIHAIQKARDHGLLSYHI<PQVEPQDLDFNASHGVMSTSLPVPTLVSGESWYLWYSWKQP

Parental  PERELSRLRRLYQGHLREESG-PPPESMPKMPPATPAEASSTGQTDPQSAL
          .ERELS.L..LYQG...EESG.P..ES.PKM.P.TP.EAS.T..T.P.SAL
Retrocopy SERELSHLCQLYQGYR*EESG>PTSESVPKMLPTTPVEASFTEETGP*SAL

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_1811 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 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005581	1 retrocopy	retro_chof_505,
Macropus eugenii	ENSMEUG00000012457	10 retrocopies	retro_meug_1183, retro_meug_2004, retro_meug_2124, retro_meug_215, retro_meug_610, retro_meug_648, retro_meug_696, retro_meug_712, retro_meug_717, retro_meug_734,
Macaca mulatta	ENSMMUG00000006525	1 retrocopy	retro_mmul_900,
Monodelphis domestica	ENSMODG00000015933	1 retrocopy	retro_mdom_426,
Mus musculus	ENSMUSG00000024436	1 retrocopy	retro_mmus_2036,
Nomascus leucogenys	ENSNLEG00000005224	1 retrocopy	retro_nleu_1811 ,
Oryctolagus cuniculus	ENSOCUG00000002149	2 retrocopies	retro_ocun_1307, retro_ocun_1641,
Pongo abelii	ENSPPYG00000016412	1 retrocopy	retro_pabe_2050,
Pan troglodytes	ENSPTRG00000017932	1 retrocopy	retro_ptro_1648,
Rattus norvegicus	ENSRNOG00000000804	1 retrocopy	retro_rnor_1328,
Ictidomys tridecemlineatus	ENSSTOG00000011853	1 retrocopy	retro_itri_254,
Tarsius syrichta	ENSTSYG00000003333	1 retrocopy	retro_tsyr_1769,