RetrogeneDB ID: retro_nleu_2847

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397451.1:926572..928068(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC20
• Ensembl ID: ENSNLEG00000013419
• Aliases: None
• Description: None

Sequence

>retro_nleu_2847
ATGGCACAATTCGCGTTCGAGAGTGACCTGCACTCGCTTCTTCAGTTGGATGCACCCATCCCCAGTGCACCCCCTACGCG
CTGGCAGCGCAAAGCCAAGGAAGCCACAGGCCCGGCCCCCTCACCCATGCGGGCCGCCAACCGATCCCACAGCGCCGGCA
GGACTCCGGGCCGAACTCCTGGCAAATCCAGTTCCAAGGTTCAGACCACTCCTAGCAAACCTGCTGATGACCGCTATATC
CCCCATCGCAGTGCTGCCCAGATGGAGGTGGCCAGCTTCCTCCTGAGCAAGGAGAACCAGCCTGAAAACAGCCAGACGCC
CACCAAGAAGGAACATCAGAAAGCCTGGGCTTTGAATCTGAACGGTTTTGATGTAGAGGAAGCCAAGATCCTTCGGCTCA
GTGGAAAACCACAAAATGCACCAGTGGTTACCAGAACAGACTGAAAGTACTCTACAGCCAAAAGGCCACTCCTGGCTCCA
GCCGGCAGACCTGCTGTTACATTCCTTCCCTGCCAGACCATATCCTGGATGCCCCTGAAATCCGAAATGACTACTACCTG
AACCTTGTGGACTGGAGCTCTGGGAATGTACTGGCCATGGCACTGGACAACAGTGTGTACCTGTGGAGTGCAAGCTCTGG
TGACATCCTGCACCTTTTGCAAATGGAGCAGCCTGGGGAATATGTATCCTCTGTGGCCTGGATCAAAGAGGGCAACTACT
TGGCTGTGGGCATCAGCAGTGCTGAGGTGCAGCTATGGGATGTGCAGCAGCAGAAATGGCTTCGAAATATGACCAGTCAC
TCTGCCCGAGTGGGCTCCCTAAGCTGGAACAGCTATATCCTGTCCAGTGGTTCACATTCTGGCCACATCCACCACCATGA
TGTTCGGGTAGCAGAACATCATGTGGCCACACTGAGTGGCCACAGCCAGGAAGTGTGTGGGCTGCACTGGGCCCCAGATG
GATGACATTTGGCCAGTGGTGGCAATCATAACTTGGTCAATGTGTGGCCTAGTGCTCTTGGAGAGGGTGGCTGGGTTCCT
CTGCAGACATTCACCCAGCATCAAGGGGCTGTCAAGGCCGTAGCATGGTGTCCCTGGCAGTCCAATGTCCTGGCAACAGG
AGGGTGCAGCAGTCATCGACACATTCGCATCTAGAACGTGTGCTCTGGTGCTCGTCTGAGTGCCATGGATGCCCTTTCCC
AGGTGTGCTCCATCCTCTGGTCTCCCCACTACAAGGAGCTCATCTCAGGCCATGGCTTTGCACAGAACCAGCTGGTTATT
TGGAAGTACCCAACCATGGCCAAGGTGGCTGAACTCAAAAGTCACACATCCCGGGTCCTGAGTCTGACCATGTGCCCAGA
TGGGGCCACAGTGGCATCCGCAGCAGCAGATGAGACCCTGAGGCTATGGCACTGTTTTGAGTTGGACCCTGCGTGGCAGC
GGGAGCAGGAGAAGGCCAGTGCAGCCAAAAGCAGCCTCATCCACCAAGGCATCCGC

Alignment

ORF - retro_nleu_2847 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.4 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAQFAFESDLHSLLQLDAPIPNAPPARWQRKAKEAAGPAPSPMRAANRSHSAGRTPGRTPGKSSSKVQTT
          MAQFAFESDLHSLLQLDAPIP.APP.RWQRKAKEA.GPAPSPMRAANRSHSAGRTPGRTPGKSSSKVQTT
Retrocopy MAQFAFESDLHSLLQLDAPIPSAPPTRWQRKAKEATGPAPSPMRAANRSHSAGRTPGRTPGKSSSKVQTT

Parental  PSKPGGDRYIPHRSAAQMEVASFLLSKENQPENSQTPTKKEHQKAWALNLNGFDVEEAKILRLSGKPQNA
          PSKP..DRYIPHRSAAQMEVASFLLSKENQPENSQTPTKKEHQKAWALNLNGFDVEEAKILRLSGKPQNA
Retrocopy PSKPADDRYIPHRSAAQMEVASFLLSKENQPENSQTPTKKEHQKAWALNLNGFDVEEAKILRLSGKPQNA

Parental  P-EGYQNRLKVLYSQKATPGSSRKTCRYIPSLPDRILDAPEIRNDYYLNLVDWSSGNVLAVALDNSVYLW
          P..GYQNRLKVLYSQKATPGSSR.TC.YIPSLPD.ILDAPEIRNDYYLNLVDWSSGNVLA.ALDNSVYLW
Retrocopy P<SGYQNRLKVLYSQKATPGSSRQTCCYIPSLPDHILDAPEIRNDYYLNLVDWSSGNVLAMALDNSVYLW

Parental  SASSGDILQLLQMEQPGEYVSSVAWIKEGNYLAVGTSSAEVQLWDVQQQKRLRNMTSHSARVGSLSWNSY
          SASSGDIL.LLQMEQPGEYVSSVAWIKEGNYLAVG.SSAEVQLWDVQQQK.LRNMTSHSARVGSLSWNSY
Retrocopy SASSGDILHLLQMEQPGEYVSSVAWIKEGNYLAVGISSAEVQLWDVQQQKWLRNMTSHSARVGSLSWNSY

Parental  ILSSGSRSGHIHHHDVRVAEHHVATLSGHSQEVCGLRWAPDGRHLASGGNDNLVNVWPSAPGEGGWVPLQ
          ILSSGS.SGHIHHHDVRVAEHHVATLSGHSQEVCGL.WAPDG.HLASGGN.NLVNVWPSA.GEGGWVPLQ
Retrocopy ILSSGSHSGHIHHHDVRVAEHHVATLSGHSQEVCGLHWAPDG*HLASGGNHNLVNVWPSALGEGGWVPLQ

Parental  TFTQHQGAVKAVAWCPWQSNVLATGGGTSDRHIRIWNVCSGACLSAVDAHSQVCSILWSPHYKELISGHG
          TFTQHQGAVKAVAWCPWQSNVLATGG..S.RHIRI.NVCSGA.LSA.DA.SQVCSILWSPHYKELISGHG
Retrocopy TFTQHQGAVKAVAWCPWQSNVLATGGCSSHRHIRI*NVCSGARLSAMDALSQVCSILWSPHYKELISGHG

Parental  FAQNQLVIWKYPTMAKVAELKGHTSRVLSLTMSPDGATVASAAADET-RLWRCFELDPARRREREKASAA
          FAQNQLVIWKYPTMAKVAELK.HTSRVLSLTM.PDGATVASAAADET.RLW.CFELDPA..RE.EKASAA
Retrocopy FAQNQLVIWKYPTMAKVAELKSHTSRVLSLTMCPDGATVASAAADETLRLWHCFELDPAWQREQEKASAA

Parental  KSSLIHQGIR
          KSSLIHQGIR
Retrocopy KSSLIHQGIR

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_2847 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006680	2 retrocopies	retro_chof_2172, retro_chof_2286,
Callithrix jacchus	ENSCJAG00000003414	1 retrocopy	retro_cjac_1608,
Homo sapiens	ENSG00000117399	1 retrocopy	retro_hsap_4187,
Gorilla gorilla	ENSGGOG00000010419	1 retrocopy	retro_ggor_96,
Mus musculus	ENSMUSG00000006398	1 retrocopy	retro_mmus_1536,
Nomascus leucogenys	ENSNLEG00000013419	1 retrocopy	retro_nleu_2847 ,
Pongo abelii	ENSPPYG00000001448	1 retrocopy	retro_pabe_3428,
Pan troglodytes	ENSPTRG00000000634	1 retrocopy	retro_ptro_2843,
Tarsius syrichta	ENSTSYG00000012703	3 retrocopies	retro_tsyr_1560, retro_tsyr_442, retro_tsyr_938,
Tursiops truncatus	ENSTTRG00000010813	1 retrocopy	retro_ttru_1309,