RetrogeneDB ID: retro_nleu_2936

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397494.1:817921..818684(+)
• Located in intron of: ENSNLEG00000015744

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB5
• Ensembl ID: ENSNLEG00000014891
• Aliases: None
• Description: Proteasome subunit beta type [Source:UniProtKB/TrEMBL;Acc:G1RXZ4]

Sequence

>retro_nleu_2936
GTGAACCAGTGCAGGTTTTCTGGACTCACAGTTTATGCAGATCTGCTGGATCTGGGTCCAGGGAGTCCCAGTGATGGGCT
GAGCCTGGCCATGCCCAGCTGGGGAGTCTCAGAGGAGCGGGAAATCAAAATGCTTCATGGAATCACCACCCTGGTCTTCA
AGTTCTGGCATGGAGTCATAGCTGCAGCAGACTATAGGGCTACAGTGGGTGCTTACATTGCCTCCGGATGGTAAAGAAGG
TGACAGAGATCAACCCCTACCCGAAGCCATCATGGCTAGGGGCACAGGGAACTGTAGCTTCTGAGAATGGCTGTTGGCTT
GGCAAAGTCAAATGTATGAGCTTTGAAATAAGGACCGCATCCCTGTAACAGCTGCCTCCAAGCTGCTTGCCAACATGTTG
TGTCAGGACAAAGGCATGGGGCTGTCCATGGGCAACATGATCTGTGGCTGGGATAGAAGAGGCCCTGGCCTCTGCTACAT
GGACGCTGAAGGGAATCAGATCTCGGGGGCCACCTTCTCTGTAGGTTCTGGCTCTGTGTATGCATATGGGGTTATGAATC
AGGGCTACTCCTATAACCTGGAAATGGGGCAGGCCTATGATCTGGCCCATGAGATGAGCTACCAAGCCATCTACCAAGCC
ACCTGCATAGATGCCTACTCAGGAGGTGCTGCTAACCTCTACCATGTGCAGGAGGATGGCTGGATCCAAGTCTCCAGTGA
CAACGCAGTTGATCTTCATGACAAGTATGATGGATCTACCCCA

Alignment

ORF - retro_nleu_2936 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.6 %
• Parental protein coverage: 95.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VNQRGFFGLGGRADLLDLGPGSLRDGLSLAAPGWGVPEEPGIEMLHGTTTLAFKFRHGVIVAADSRATAG
          VNQ..F.GL...ADLLDLGPGS..DGLSLA.P.WGV.EE..I.MLHG.TTL.FKF.HGVI.AAD.RAT.G
Retrocopy VNQCRFSGLTVYADLLDLGPGSPSDGLSLAMPSWGVSEEREIKMLHGITTLVFKFWHGVIAAADYRATVG

Parental  AYIAS-QTVKKVIEIN-PYLLGTMAGGAADCSFWERLLARQCRIYELRNKERISVAAASKLLANMVYQYK
          AYIAS...VKKV.EIN.P.....MA.G...CSF.E.LLA.Q...YEL.NK.RI.V.AASKLLANM..Q.K
Retrocopy AYIAS<RMVKKVTEIN<PLPEAIMARGTGNCSF*EWLLAWQSQMYEL*NKDRIPVTAASKLLANMLCQDK

Parental  GMGLSMGTMICGWDKRGPGLYYVDSEGNRISGATFSVGSGSVYAYGVMDRGYSYDLEVEQAYDLAR----
          GMGLSMG.MICGWD.RGPGL.Y.D.EGN.ISGATFSVGSGSVYAYGVM..GYSY.LE..QAYDLA.....
Retrocopy GMGLSMGNMICGWDRRGPGLCYMDAEGNQISGATFSVGSGSVYAYGVMNQGYSYNLEMGQAYDLAHEMSY

Parental  RAIYQATYRDAYSGGAVNLYHVREDGWIRVSSDNVADLHEKYSGSTP
          .AIYQAT..DAYSGGA.NLYHV.EDGWI.VSSDN..DLH.KY.GSTP
Retrocopy QAIYQATCIDAYSGGAANLYHVQEDGWIQVSSDNAVDLHDKYDGSTP

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_2936 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008299	4 retrocopies	retro_cjac_1983, retro_cjac_35, retro_cjac_3888, retro_cjac_4076,
Homo sapiens	ENSG00000100804	2 retrocopies	retro_hsap_1634, retro_hsap_95,
Gorilla gorilla	ENSGGOG00000026856	2 retrocopies	retro_ggor_1232, retro_ggor_156,
Latimeria chalumnae	ENSLACG00000015194	1 retrocopy	retro_lcha_3,
Macropus eugenii	ENSMEUG00000003572	1 retrocopy	retro_meug_28,
Myotis lucifugus	ENSMLUG00000014281	1 retrocopy	retro_mluc_1428,
Macaca mulatta	ENSMMUG00000006007	1 retrocopy	retro_mmul_1558,
Mus musculus	ENSMUSG00000022193	1 retrocopy	retro_mmus_2887,
Nomascus leucogenys	ENSNLEG00000014891	2 retrocopies	retro_nleu_1063, retro_nleu_2936 ,
Oryctolagus cuniculus	ENSOCUG00000013109	1 retrocopy	retro_ocun_176,
Pongo abelii	ENSPPYG00000005654	1 retrocopy	retro_pabe_171,
Sus scrofa	ENSSSCG00000002036	1 retrocopy	retro_sscr_616,