RetrogeneDB ID: retro_ptro_2843

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:85839436..85840891(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000021078
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CDC20
• Ensembl ID: ENSPTRG00000000634
• Aliases: None
• Description: Pan troglodytes cell division cycle 20 homolog (S. cerevisiae) (CDC20), mRNA. [Source:RefSeq mRNA;Acc:NM_001243972]

Sequence

>retro_ptro_2843
CTTCAACTGGATGCACCCATCCCCAATGCACCCCCTGCTCGCTGGCAGCGCAAAGCCAAGAAAGCCACAGGCCCGGCGCC
CTCACCCATGCGGGCCGCCAACCGATCCCACGGCGCCGGCAGGACTCCAGGCCGAACTCCTGGCAAATCCAGTTCCAAGG
GTCAGACCACTCCTAGCAAACCTGGCGGTAACCGCTATATCCCCCCTCACAGTGCTGCCCAGATGGAGGTGGCCAGCTTC
CTCCTGAGAAAGGAGAACCAGCCTGAAAACAGCCAGACGCCCACCAAGAAGGAACATCAGAAAGCCTGGACTTTGAACCT
GAACGGTTTTGATGTAGAGGAAGCCAAGATCCTTCGGCTCAGTGGAAAACCACAAAATGCGCCAGAGGGTTACCAGAACA
GACTGAAAGTACTCTACAGCCAAAAGGCCACTCCTGGCTCCAGCCGGAAGACCTACCATTACATTCCTTCCCTGCCAGAC
CATAACCTGGATGCCCCTGAAATCCGAAATGACTACTACCTGAACCTTGTGGACTGGAGCTCTGGGAATGTATTGGCCGT
GGCGCTGGACAACAGTGTGTACCTGTGGAGCGCAAGCTCTGGTGACATCCTGCAGCTTTTGCAAATGGAGCAGACTGGGA
AATATGTATACTCTGCGGCCTGGATCAAAGAGGGCAACTACTTGGCTGTGGGCATCAGCAGTGCTGAGGTGCAGCTATGG
GATGTGCAGCAGCAGAAACGGCTTCGAAATATGACCAGTCACTCTGCCCGAGTGGGCTCCCTAAGCTGGAACAGCTATAT
CCTATCCAGTGGTTCACATTCTGGCCACATCCACCACCATGATGTTCGGGTGGCAGAACACCACGTGGCCACACTGAGTG
GCCACAGCCAGGAAGTGTGTGGGCTGCGCTGGGTCCCAGATGGACGACATTTGGCCAGTGGTGGCAATGATAACTTGGTC
AAAGTGTGGCCTAGTGCTCTTGGAGAGGGTGGCTGGGTTCCTCTGCAGACATTCACCCTTCAAGGGGCTGTCAAGGCCGT
AGCATGGTGTCCCTGGCAGTCCAATGTCCCGGCAACAGGAGGGGGCACCAGTGATCGACATATTTGCATCTGGAACGTGT
GCTCTGGGGCCTGTCTGAGTGCCGTGGATGCCCTTTCCCAGGTGTGCTCCATCCTCTGGTCTCCCCACTACAAGGAGCTC
ATCTCAGGCCATGGCTTTGCACAGAACCAGCTGGTTATTTGGAAGTACCCAACCATGGCCAAGGTGGCTGAACTCAAAGG
TCACACATCCCGGGTCCTGACTCTGACCATGAGCCCAGATGGGGCCACAGTGGCATCTGCAGCAGCAGATGAGACCCCGA
GGCTATGGCACTGTTTTGAGTTGGACCCTGTGTGGCGGCGGGAGCGGGAGAAGGCCAGTGCAGCCAAAAGCAGCTTCATC
CACCAAGGCATCCGC

Alignment

ORF - retro_ptro_2843 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.56 %
• Parental protein coverage: 99.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLLDAPIP-APPARWQRKVE-AAGPAPSPMRAANRSHSAGRTPGRTPGKSSSKVQTTPSNPGGDRYIPHR
          L.LDAPIP.APPARWQRK...A.GPAPSPMRAANRSH.AGRTPGRTPGKSSSK.QTTPS.PGG.RYIP..
Retrocopy LQLDAPIPNAPPARWQRKAKKATGPAPSPMRAANRSHGAGRTPGRTPGKSSSKGQTTPSKPGGNRYIPPH

Parental  SAAQMRVASFLXSKENQPENSQTPTKKEHQKAWALNLNGFDVEEAKILRLSGKPQNAPEGYQNRLKVLYS
          SAAQM.VASFL..KENQPENSQTPTKKEHQKAW.LNLNGFDVEEAKILRLSGKPQNAPEGYQNRLKVLYS
Retrocopy SAAQMEVASFLLRKENQPENSQTPTKKEHQKAWTLNLNGFDVEEAKILRLSGKPQNAPEGYQNRLKVLYS

Parental  QKATPGSSRKTCRYIPSLPDRILDAPEIRNDYYLNLVDWSSGNVLAVALDNSVYLWSASSGDILQLLQME
          QKATPGSSRKT..YIPSLPD..LDAPEIRNDYYLNLVDWSSGNVLAVALDNSVYLWSASSGDILQLLQME
Retrocopy QKATPGSSRKTYHYIPSLPDHNLDAPEIRNDYYLNLVDWSSGNVLAVALDNSVYLWSASSGDILQLLQME

Parental  QPGEYISSVAWIKEGNYLAVGTSSAEVQLWDVQQQKRLRNMTSHSARVGSLSWNSYILSSGSRSGHIHHH
          Q.G.Y..S.AWIKEGNYLAVG.SSAEVQLWDVQQQKRLRNMTSHSARVGSLSWNSYILSSGS.SGHIHHH
Retrocopy QTGKYVYSAAWIKEGNYLAVGISSAEVQLWDVQQQKRLRNMTSHSARVGSLSWNSYILSSGSHSGHIHHH

Parental  DVRVAEHHVATLSGHSQEVCGLRWAPDGRHLASGGNDNLVNVWPSAPGEGGWVPLQTFTQHQGAVKAVAW
          DVRVAEHHVATLSGHSQEVCGLRW.PDGRHLASGGNDNLV.VWPSA.GEGGWVPLQTFT..QGAVKAVAW
Retrocopy DVRVAEHHVATLSGHSQEVCGLRWVPDGRHLASGGNDNLVKVWPSALGEGGWVPLQTFTL-QGAVKAVAW

Parental  CPWQSNVLATGGGTSDRHIRIWNVCSGACLSAVDAHSQVCSILWSPHYKELISGHGFAQNQLVIWKYPTM
          CPWQSNV.ATGGGTSDRHI.IWNVCSGACLSAVDA.SQVCSILWSPHYKELISGHGFAQNQLVIWKYPTM
Retrocopy CPWQSNVPATGGGTSDRHICIWNVCSGACLSAVDALSQVCSILWSPHYKELISGHGFAQNQLVIWKYPTM

Parental  AKVAELKGHTSRVLSLTMSPDGATVASAAADETLRLWRCFELDPARRREREKASAAKSSLIHQGIR
          AKVAELKGHTSRVL.LTMSPDGATVASAAADET.RLW.CFELDP..RREREKASAAKSS.IHQGIR
Retrocopy AKVAELKGHTSRVLTLTMSPDGATVASAAADETPRLWHCFELDPVWRREREKASAAKSSFIHQGIR

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	0.38 RPM	1.45 RPM
SRP007412_cerebellum	0.93 RPM	1.90 RPM
SRP007412_heart	0.00 RPM	0.55 RPM
SRP007412_kidney	0.44 RPM	2.85 RPM
SRP007412_liver	0.03 RPM	3.40 RPM
SRP007412_testis	1.90 RPM	79.46 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2843 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2843 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2843 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4187
Gorilla gorilla	retro_ggor_96
Pongo abelii	retro_pabe_3428

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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,