RetrogeneDB ID: retro_nleu_843

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397274.1:19061090..19061798(-)
• Located in intron of: ENSNLEG00000016942

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM64A
• Ensembl ID: ENSNLEG00000009164
• Aliases: None
• Description: None

Sequence

>retro_nleu_843
ATGGCTTCTCGGTGGCAGGGTGTAGGGGCCTCTGTGCGCCGGAGATCTCTCCAGTACCAGGAGCAGCTCAAGGACAGCAA
GGAGCTGCAGCCTGTGGCCAGCCATCCAGCAGACCCCTGCCACAGCCCTGGGTTCCGTGCGCAGACAGTTCCAAAGGAGG
CTGCCCCTGACAGCCGTCAACCTCAACCTCTGGGGAGACCCCTCCTGGCAACACTTGGAAACCCCAGAGCCAAGGCAGCA
GAGCCTCCAGGCTGCAGATAGCTCAGCTAACAGTGCCTCAGGTGCCAAGTCCCAGAGAATCCAGGATCCTGACACCAAAT
GGCTGGTGGAGACTCAGGTGAAGGCCAGGAGGAGGAAGAGAGGGGCACAGAAGAGCAGTGGATCCCAGACTCACAGATGA
GCCCGAAGACCACCCAAGTGTCCTGAGGTACCCTTGCACACTCAGCCGCAGACCCCTGGGAGAAGGAGCATCAGTGCCTC
TCTGCCCGTATGGGTTCGTGTACCCACTCACTAAGGCGGTTGAGGCGGGAGTGTGCGTTTTAGAGCCCTTACCCCTTGAC
AGAGCCCCTCTGCTCTCCCAGTGAGTCTGACAGTGACCTACAGCCTGTGGAGGCAGAAATTCAGCATCTCCAGAAGCTGT
CCCAAGAGCTGGACGAAGCCATTATGGCAGAAGAGAGTGGTGATATGAGCATCTCTCTCATTCATGAC

Alignment

ORF - retro_nleu_843 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.1 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASRWQSMGTSVRRRSLQHQEQLEDSKELQPVVSH-QETSAGALGSLCRQFQRRLPLRAVNLNLRAGPSW
          MASRWQ..G.SVRRRSLQ.QEQL.DSKELQPV.SH.Q.T.A.ALGS..RQFQRRLPL.AVNLNL...PSW
Retrocopy MASRWQGVGASVRRRSLQYQEQLKDSKELQPVASH>QQTPATALGSVRRQFQRRLPLTAVNLNLWGDPSW

Parental  KRLETPEPGQQGLQAAARSAKSALGAVSQRIQESCQSGTKWLVETQVKARRRKRGAQKGRGSPTH-SLSQ
          ..LETPEP.QQ.LQAA..SA.SA.GA.SQRIQ......TKWLVETQVKARRRKRGAQK..GS.TH...S.
Retrocopy QHLETPEPRQQSLQAADSSANSASGAKSQRIQDP---DTKWLVETQVKARRRKRGAQKSSGSQTH<QMSP

Parental  KSTRLSGAALAHSAADPWEKEHHCLSTWMGSCAHPLRRSRREAAFRSPYSSTEPLCSPSESDSDLEPVGA
          K.T..S...LAHSAADPWEKEH.CLS..MGSC.H.LRR.RRE.AF.SPY..TEPLCSPSESDSDL.PV.A
Retrocopy KTTQVS*GTLAHSAADPWEKEHQCLSARMGSCTHSLRRLRRECAF*SPYPLTEPLCSPSESDSDLQPVEA

Parental  GIQHLQKLSQELDEAIMAEESGDI-VSLIHD
          .IQHLQKLSQELDEAIMAEESGD...SLIHD
Retrocopy EIQHLQKLSQELDEAIMAEESGDMSISLIHD

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_843 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 10 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006997	1 retrocopy	retro_amel_1136,
Homo sapiens	ENSG00000129195	3 retrocopies	retro_hsap_2371, retro_hsap_3030, retro_hsap_3071,
Gorilla gorilla	ENSGGOG00000012309	3 retrocopies	retro_ggor_1801, retro_ggor_2091, retro_ggor_2109,
Macaca mulatta	ENSMMUG00000017760	3 retrocopies	retro_mmul_1778, retro_mmul_1935, retro_mmul_959,
Mus musculus	ENSMUSG00000020808	1 retrocopy	retro_mmus_3385,
Nomascus leucogenys	ENSNLEG00000009164	3 retrocopies	retro_nleu_361, retro_nleu_725, retro_nleu_843 ,
Otolemur garnettii	ENSOGAG00000027433	1 retrocopy	retro_ogar_1490,
Pongo abelii	ENSPPYG00000007877	3 retrocopies	retro_pabe_2141, retro_pabe_2509, retro_pabe_2545,
Pan troglodytes	ENSPTRG00000008641	3 retrocopies	retro_ptro_1734, retro_ptro_2044, retro_ptro_2070,
Rattus norvegicus	ENSRNOG00000008040	1 retrocopy	retro_rnor_1325,