RetrogeneDB ID: retro_nleu_1063

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397280.1:2221381..2222003(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000014898
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1063
CTTCCTGCAGATCCATGGCCCCAGACTGGCCCATGGCACTACCACCCTGGCCTTCCGCTTCCGTCATGGAGTCATTGCTG
CAGCTGACACCCGTTCCTCCTGTGGCAGCTATGTGGCGTGTCCAGCCTCATGCAAGGTCATCCCTGTGCACCAGCACCTC
CTGGGTACCACCTCTGGCCCTCCGCCGACTGTGCTACCTGGTATCGGGTATACAGCGGGAGCTGCGGCTTCGGGAACTGA
GGGAGGGTCAGCTGCCCAGTGTGGCCAGTGCTGCAAGCTATTGTCAGCCATGAAGTCTCGATACCGGGGACTGGATCTCT
GTGTGGCCACTGCCCTGTGCGGCTGGGACTGCTCTGGCCCTGAGCTCTTCTACGTCTATAGCGACGGCACCCGCCTGCAG
GGGGACATCTTCTCTGTGGGCTCTGGATCTCCCTATGCCTACGGTGTGCTAGACCGTGGCTATCGCTACGACATGAGCAC
CCAGGAAGCCTATGCCCTGGCTCGCTGCGCCGTGGCCCACGCCACCCACCGTGATGCCTATTCAGGGGGATCTGTAGACC
TTTTCCACGTGCGGGAGAGTGGATGGGAGCAGGTGTCACGCAGTGATGCCTGTGTGCTGTAC

Alignment

ORF - retro_nleu_1063 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.36 %
• Parental protein coverage: 79.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VPEEP-GIEMLHGTTTLAFKFRHGVIVAADSRATAGAYIASQTVKKVIEINPYLLGTMAGG-AADCSFWE
          .P..P.G....HGTTTLAF.FRHGVI.AAD.R...G.Y.A.....KVI.....LLGT..G...ADC..W.
Retrocopy LPADP>GPRLAHGTTTLAFRFRHGVIAAADTRSSCGSYVACPASCKVIPVHQHLLGTTSGP<SADCATWY

Parental  RLLARQC-RIYELRNKERISVAAAS-KLLANMVYQYKGMGLSMGTMICGWDKRGPGLYYVDSEGNRISGA
          R.....C.R..ELR.....SVA.A..KLL..M...Y.G..L...T..CGWD..GP.L.YV.S.G.R..G.
Retrocopy RVYSGSC<RLRELREGQLPSVASAA<KLLSAMKSRYRGLDLCVATALCGWDCSGPELFYVYSDGTRLQGD

Parental  TFSVGSGSVYAYGVMDRGYSYDLEVEQAYDLARRAIYQATYRDAYSGGAVNLYHVREDGWIRVSSDNVAD
          .FSVGSGS.YAYGV.DRGY.YD.....AY.LAR.A...AT.RDAYSGG.V.L.HVRE.GW..VS......
Retrocopy IFSVGSGSPYAYGVLDRGYRYDMSTQEAYALARCAVAHATHRDAYSGGSVDLFHVRESGWEQVSRSDACV

Parental  LH
          L.
Retrocopy LY

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_1063 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,