RetrogeneDB ID: retro_pabe_3428

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:82212017..82213514(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC20
• Ensembl ID: ENSPPYG00000001448
• Aliases: None
• Description: cell division cycle 20 [Source:HGNC Symbol;Acc:1723]

Sequence

>retro_pabe_3428
ATGACACAATTCGCGTTCGAGAGTGACCTGCACTCGCTGCTTCAGCTGGATGCACCCATCCCCAATGCACTCCCTGCGCC
CTGGCAGCGCAAAGCCAAGGAAGCCGCAGGCCCGGCCCCCTCACCCATGCGGGCCGCCAGCCGATCCCACAGCGCCGGCA
GGACTCCGGGCCGAACTCCTGGCAAATCCAGTTCCAAGGTACAGACCACTCCTAGCAAACCTGGCGGTGACCGCTATATC
CCCCATCGCAGTGCTGACCAGATGGAGGTGGCCAGCTTCCTCCTGAGCAAGGAGAACCAGCCTGAAAACAGCCAGACGCC
CACCAAGAAGGAACATCAGAAAGCCTGGACTTTGAACCTGAACGGTTTTGATGTAGAAGAAGCCAAGATCCTTCGGCTCA
GTGGAAAACCACAAAATGCGCCAGAGGGTTACCAGAACAGACTGAAAGTACTGTACAGCCAAAAGGCCACTCCTGGCTCC
AGCCAGAAGGCCTGCCATTACATTCCTTCCCTGCCAGACCATATCCTGGATGCCCCTGAAATCTGAAATGACTACTACCT
GTACCTTGTGGATAGGAGCTCTGGGAATTTACTGGCCGTGGCACTGGACAACAGTGTGTACCCATGGAGCGCAAGCTCTG
GTGACATCCTGCAGCTTTTGCAAATGGAGCAGCCTGGGGAATATGTATCCTCTGTGGCCTGGATCAAAGAGGGCAACTAC
TTGGCTGTGGGCATCAGCAGTGCTGAGGTGCAGCTATGGGATGTGCAGCAGCAGAAACAGCTTCGAAATATGACCAGTCA
CTCTGCCCGAGTGGGCTCCCTAAGCTGGAACAGCTACATCCTGTCCAGTGGTTCACATTCTGGCCACATCCACCACCATG
ATGTTCAGGTAGCAGAACACCATGTGGCCACACTGAGTGGCCACAGCCAGGAAGTGTGTGGGCTGCACTGAGCCCCAAAT
GGACGACATTTGGCCAGTGGTGGCAATGATAACTTGGTCAATGTGTGGCCTAGTGCTCTTGGAGAGGGTGGCTGGGTTCC
TCTGCAGACATTCACCCAGCATCAAGGGGCTGTCAAGGCCGTAGCATGGTGTCCCTGGCAGTCCAATGTCCTGGCAACAG
GAGGGGGCACCAGTGATCAACACACTCGCATCTGGAACGTGTGCTTTGGGGCCTGTCTGAGTGCCGTAGATGCCCTTTCC
CAGGTGTGCTCCATCCTCTGGTCTCCCCACTACAAGGAGCTCATCTCAGGCCATGGCTTTGCACAGAACCAGCTGGTCTT
TTGGAAGTACCCAACAATGGCCAAGGTGGCTGAACTCAAAGGTCACACATCCAGGGTCCTGAGTCTGACCATGAGCCCAG
ATGGGGCCACAGTAGCATCCGCAGCAGCAGATGAGACCCTGAGGCTATGGCACTGTTTTGAGTTGGACCCTGCGTGGCGG
CGGGAGCGGGAGAAGGCCAGCGCAGTCAAAAGCAGCCTCATCCACCAAGGCATCCGC

Alignment

ORF - retro_pabe_3428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.79 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAQFAFESDLHSLLQLDAPIPNAPPARWQRKAKEAAGPAPSPMRAANRSHSAGRTPGRTPGKSSSKVQTT
          M.QFAFESDLHSLLQLDAPIPNA.PA.WQRKAKEAAGPAPSPMRAA.RSHSAGRTPGRTPGKSSSKVQTT
Retrocopy MTQFAFESDLHSLLQLDAPIPNALPAPWQRKAKEAAGPAPSPMRAASRSHSAGRTPGRTPGKSSSKVQTT

Parental  PSKPGGDRYIPHRSAAQMEVASFLLSKENQPENSQTPTKKEHQKAWALNLNGFDVEEAKILRLSGKPQNA
          PSKPGGDRYIPHRSA.QMEVASFLLSKENQPENSQTPTKKEHQKAW.LNLNGFDVEEAKILRLSGKPQNA
Retrocopy PSKPGGDRYIPHRSADQMEVASFLLSKENQPENSQTPTKKEHQKAWTLNLNGFDVEEAKILRLSGKPQNA

Parental  PEGYQNRLKVLYSQKATPGSSRKTCRYIPSLPDRILDAPEIRNDYYLNLVDWSSGNVLAVALDNSVYLWS
          PEGYQNRLKVLYSQKATPGSS.K.C.YIPSLPD.ILDAPEI.NDYYL.LVD.SSGN.LAVALDNSVY.WS
Retrocopy PEGYQNRLKVLYSQKATPGSSQKACHYIPSLPDHILDAPEI*NDYYLYLVDRSSGNLLAVALDNSVYPWS

Parental  ASSGDILQLLQMEQPGEYVSSVAWIKEGNYLAVGTSSAEVQLWDVQQQKRLRNMTSHSARVGSLSWNSYI
          ASSGDILQLLQMEQPGEYVSSVAWIKEGNYLAVG.SSAEVQLWDVQQQK.LRNMTSHSARVGSLSWNSYI
Retrocopy ASSGDILQLLQMEQPGEYVSSVAWIKEGNYLAVGISSAEVQLWDVQQQKQLRNMTSHSARVGSLSWNSYI

Parental  LSSGSRSGHIHHHDVRVAEHHVATLSGHSQEVCGLRWAPDGRHLASGGNDNLVNVWPSAPGEGGWVPLQT
          LSSGS.SGHIHHHDV.VAEHHVATLSGHSQEVCGL..AP.GRHLASGGNDNLVNVWPSA.GEGGWVPLQT
Retrocopy LSSGSHSGHIHHHDVQVAEHHVATLSGHSQEVCGLH*APNGRHLASGGNDNLVNVWPSALGEGGWVPLQT

Parental  FTQHQGAVKAVAWCPWQSNVLATGGGTSDRHIRIWNVCSGACLSAVDAHSQVCSILWSPHYKELISGHGF
          FTQHQGAVKAVAWCPWQSNVLATGGGTSD.H.RIWNVC.GACLSAVDA.SQVCSILWSPHYKELISGHGF
Retrocopy FTQHQGAVKAVAWCPWQSNVLATGGGTSDQHTRIWNVCFGACLSAVDALSQVCSILWSPHYKELISGHGF

Parental  AQNQLVIWKYPTMAKVAELKGHTSRVLSLTMSPDGATVASAAADETLRLWRCFELDPARRREREKASAAK
          AQNQLV.WKYPTMAKVAELKGHTSRVLSLTMSPDGATVASAAADETLRLW.CFELDPA.RREREKASA.K
Retrocopy AQNQLVFWKYPTMAKVAELKGHTSRVLSLTMSPDGATVASAAADETLRLWHCFELDPAWRREREKASAVK

Parental  SSLIHQGIR
          SSLIHQGIR
Retrocopy SSLIHQGIR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.06 RPM	0.50 RPM
SRP007412_cerebellum	0.00 RPM	0.36 RPM
SRP007412_heart	0.03 RPM	0.60 RPM
SRP007412_kidney	0.00 RPM	1.86 RPM
SRP007412_liver	0.00 RPM	0.61 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3428 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3428 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3428 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4187
Pan troglodytes	retro_ptro_2843
Gorilla gorilla	retro_ggor_96

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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,