RetrogeneDB ID: retro_nleu_200

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397261.1:74135339..74135965(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000017972
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ENSG00000154917
• Ensembl ID: ENSNLEG00000017098
• Aliases: None
• Description: None

Sequence

>retro_nleu_200
GTGTCCGCGGGCGGAGACTTCGGGAATCCGCTGAGGAAATTCAAGCTGGTGTTCCTGGGGGAGCAAAGCGTTGCAAAGAC
ATCTTTGATCACCAGATTCATGTATGACAGTTTTGACGACACCTATCAGGCAACAATTTGGCATTGACTTTTTATCGAAA
ACTATGTACTTGGAGGATGGAACAATCAGGCTTCGGGCTGTGGGATACTGCGGGTCAGGAACGTCTCCGTAGCCTCATTC
CCAGTTACATCCGTGATTCTGCTGCAGCTGTAGTAGTTTACGATATCACAAATGTTAACTCCTTCCAGCAAACTACAAAG
TGGATTGATGATGTCAGAACAGAAAGAGGAAGTGATGTTATCATCACGCTAGTAGGAAATAGAACAGATCTTGCTGACAA
GAGGCAAATGTCAATTGAGGAGGGAGAGAGGAAAGCCAAAGAGCTGAATGTTGTGTTTATTGAAACTAGTGCAAAAGCTG
CATACAATGTAAAGCAGCTCTTTCGACGTGTAGCAGCAGCTTTGATGGGAATGGAAAGCACACAGGACAGAAGCAGAGAA
GACACGAGTGATAAAAAACTGGAAACGCCTCAGGAGCAACCAGTCAGTGAAGGAGGCTGTTCCTGC

Alignment

ORF - retro_nleu_200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSAGGDFGNPLRKFKLVFLGEQSVGKTSLITRFMYDSFDNTYQATI-GIDFLSKTMYLEDRTVRLQ-LWD
          .SAGGDFGNPLRKFKLVFLGEQSV.KTSLITRFMYDSFD.TYQATI.GIDFLSKTMYLED.T.RL..LWD
Retrocopy VSAGGDFGNPLRKFKLVFLGEQSVAKTSLITRFMYDSFDDTYQATI>GIDFLSKTMYLEDGTIRLR>LWD

Parental  TAGQERFRSLIPSYIRDSTVAVVVYDITNVNSFQQTTKWIDDVRTERGSDVIIMLVGNKTDLADKRQVSI
          TAGQER.RSLIPSYIRDS..AVVVYDITNVNSFQQTTKWIDDVRTERGSDVII.LVGN.TDLADKRQ.SI
Retrocopy TAGQERLRSLIPSYIRDSAAAVVVYDITNVNSFQQTTKWIDDVRTERGSDVIITLVGNRTDLADKRQMSI

Parental  EEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAALPGMESTQDRSREDMIDIKLEKPQEQPVSEGGCSC
          EEGERKAKELNV.FIETSAKA.YNVKQLFRRVAAAL.GMESTQDRSRED..D.KLE.PQEQPVSEGGCSC
Retrocopy EEGERKAKELNVVFIETSAKAAYNVKQLFRRVAAALMGMESTQDRSREDTSDKKLETPQEQPVSEGGCSC

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_200 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 7 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000992	1 retrocopy	retro_chof_859,
Homo sapiens	ENSG00000175582	1 retrocopy	retro_hsap_7,
Mus musculus	ENSMUSG00000030704	1 retrocopy	retro_mmus_2400,
Nomascus leucogenys	ENSNLEG00000017098	1 retrocopy	retro_nleu_200 ,
Ochotona princeps	ENSOPRG00000010355	6 retrocopies	retro_opri_1082, retro_opri_1085, retro_opri_1095, retro_opri_1118, retro_opri_247, retro_opri_858,
Pongo abelii	ENSPPYG00000003663	3 retrocopies	retro_pabe_2097, retro_pabe_2191, retro_pabe_3537,
Ictidomys tridecemlineatus	ENSSTOG00000023497	3 retrocopies	retro_itri_1743, retro_itri_1827, retro_itri_1885,