RetrogeneDB ID: retro_hsap_4187

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:89626569..89628063(+)
• Located in intron of: ENSG00000269994

Retrocopy information

• Ensembl ID: ENSG00000231007
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CDC20
• Ensembl ID: ENSG00000117399
• Aliases: CDC20, CDC20A, bA276H19.3, p55CDC
• Description: cell division cycle 20 [Source:HGNC Symbol;Acc:1723]

Sequence

>retro_hsap_4187
CTGGCACAATTCGCGTTCGAGAGTGACCTGCACTCGCTGCTTCAACTGGATGCACCCATCCCCAATGCACCCCCTGCTCG
CTGGCAGCGCAAAGCCAAGAAAGCCACAGGCCCGGCCCCCTCACCCATGCGGGCCGCCAACCGATCCCACAGCGCCAGCA
GGACTCCGGGCCGAACTCCTGGCAAATCCAGTTCCAAGGTTCAGACCACTCCTAGCAAACCTGGCGGTGACCGCTATATC
CCCCATCGCAGTGCTGCCCAGATGGAGGTTGCCAGCTTCCTCCTGAGCAAGGAGAACCAGCCTGAAAACAGCCAGACGCC
CACCAAGAAGGAACATCAGAAAGCCTGGACTTTGAACCTGAACGGTTTTGATGTAGAGGAAGCCAAGATCCTTCGGCTCA
GTGGAAAACCACAAAATGCGCCAGAGGGTTACCAGAACAGACTGAAAGTACTCTACAGCCAAAAGGCCACTCCTGGCTCC
AGCCGGAAGACCTACCATTACATTCCTTCCCTGCCAGACCATAACCTGGATGCCCCTGAAATCCGAAATGACTACTACCT
GAATCTTGTGGACTGGAGCTCTGGGAATGTATTGGCCGTGGCGCTGGACAACAGTGTGTACCTGTGGAGCGCAAGCTCTG
GTGACATCCTGCAGCTTTTGCAAATGGAGCAGACTGGGAAATATGTATCCTCTGCGGCCTGGATCAAAGAGGGCAACTAC
TTGGCTGTGGGCATCAGCAGTGCTGAGGTGCAGCTTTGGGATGTGCAGCAGCAGAAACGGCTTCGAAATATGACCATTCA
CTCTGCCCGAGTGGGCTCCCTAAGCTGGAACAGCTATATCCTATCCAGTGGTTCACATTCTGGCCACATCCACCACCATG
ATGTTCGGGTAGCAGAACACCACGTGGCCACACTGAGTGGCCACAGCCAGGAAGTGTGTGGGCTGCGCTGGGTCCCAGAT
GGACGACATTTGGCCAGTGGTGGCAATGATAACTTGGTCAAAGTGTGGCCTAGTGCTCTTGGAGAGGGTGGCTGGGTTCC
TCTGCAGACATTCACCCTTCAAGGGGCTGTCAAGGCCGTAGCATGGTGTCCCTGGAAGTCCAATGTCCCGGCAACAGGAG
GGGGCACCAGTGATCGACACATTTGCATCTGGAACGTGTGCTCTGGGGCCTGTCTGAGTGCCGTGGATGCCCTTTCCCAG
GTGTGCTCCACCCTCTGGTCTCCCCACTACAAGGAGCTCATCTCAGGCCATGGCTTTGCACAGAACCAGCTGGTTATTTG
GAAGTACCCAACCATGGCCAAGGTGGCTGAACTCAAAGGTCACACATCCCGGGTCCTGACTCTGACCATGAGCCCAGATG
GGGCCACAGTGGCATCTGCAGCAGCAGATGAGACCCCGAGGCTATGGCACTGTTTTGAGTTGGACCCTGTGTGGCGGCGG
GAGCGGGAGAAGGCCAGTGCAGCCAAAAGCAGCTTCATCCACCAAGGCATCCGC

Alignment

ORF - retro_hsap_4187 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAQFAFESDLHSLLQLDAPIPNAPPARWQRKAKEAAGPAPSPMRAANRSHSAGRTPGRTPGKSSSKVQTT
          .AQFAFESDLHSLLQLDAPIPNAPPARWQRKAK.A.GPAPSPMRAANRSHSA.RTPGRTPGKSSSKVQTT
Retrocopy LAQFAFESDLHSLLQLDAPIPNAPPARWQRKAKKATGPAPSPMRAANRSHSASRTPGRTPGKSSSKVQTT

Parental  PSKPGGDRYIPHRSAAQMEVASFLLSKENQPENSQTPTKKEHQKAWALNLNGFDVEEAKILRLSGKPQNA
          PSKPGGDRYIPHRSAAQMEVASFLLSKENQPENSQTPTKKEHQKAW.LNLNGFDVEEAKILRLSGKPQNA
Retrocopy PSKPGGDRYIPHRSAAQMEVASFLLSKENQPENSQTPTKKEHQKAWTLNLNGFDVEEAKILRLSGKPQNA

Parental  PEGYQNRLKVLYSQKATPGSSRKTCRYIPSLPDRILDAPEIRNDYYLNLVDWSSGNVLAVALDNSVYLWS
          PEGYQNRLKVLYSQKATPGSSRKT..YIPSLPD..LDAPEIRNDYYLNLVDWSSGNVLAVALDNSVYLWS
Retrocopy PEGYQNRLKVLYSQKATPGSSRKTYHYIPSLPDHNLDAPEIRNDYYLNLVDWSSGNVLAVALDNSVYLWS

Parental  ASSGDILQLLQMEQPGEYISSVAWIKEGNYLAVGTSSAEVQLWDVQQQKRLRNMTSHSARVGSLSWNSYI
          ASSGDILQLLQMEQ.G.Y.SS.AWIKEGNYLAVG.SSAEVQLWDVQQQKRLRNMT.HSARVGSLSWNSYI
Retrocopy ASSGDILQLLQMEQTGKYVSSAAWIKEGNYLAVGISSAEVQLWDVQQQKRLRNMTIHSARVGSLSWNSYI

Parental  LSSGSRSGHIHHHDVRVAEHHVATLSGHSQEVCGLRWAPDGRHLASGGNDNLVNVWPSAPGEGGWVPLQT
          LSSGS.SGHIHHHDVRVAEHHVATLSGHSQEVCGLRW.PDGRHLASGGNDNLV.VWPSA.GEGGWVPLQT
Retrocopy LSSGSHSGHIHHHDVRVAEHHVATLSGHSQEVCGLRWVPDGRHLASGGNDNLVKVWPSALGEGGWVPLQT

Parental  FTQHQGAVKAVAWCPWQSNVLATGGGTSDRHIRIWNVCSGACLSAVDAHSQVCSILWSPHYKELISGHGF
          FT..QGAVKAVAWCPW.SNV.ATGGGTSDRHI.IWNVCSGACLSAVDA.SQVCS.LWSPHYKELISGHGF
Retrocopy FTL-QGAVKAVAWCPWKSNVPATGGGTSDRHICIWNVCSGACLSAVDALSQVCSTLWSPHYKELISGHGF

Parental  AQNQLVIWKYPTMAKVAELKGHTSRVLSLTMSPDGATVASAAADETLRLWRCFELDPARRREREKASAAK
          AQNQLVIWKYPTMAKVAELKGHTSRVL.LTMSPDGATVASAAADET.RLW.CFELDP..RREREKASAAK
Retrocopy AQNQLVIWKYPTMAKVAELKGHTSRVLTLTMSPDGATVASAAADETPRLWHCFELDPVWRREREKASAAK

Parental  SSLIHQGIR
          SS.IHQGIR
Retrocopy SSFIHQGIR

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
bodymap2_adipose	0.10 RPM	0.80 RPM
bodymap2_adrenal	0.14 RPM	1.82 RPM
bodymap2_brain	0.80 RPM	0.70 RPM
bodymap2_breast	0.91 RPM	1.69 RPM
bodymap2_colon	0.68 RPM	1.28 RPM
bodymap2_heart	0.06 RPM	0.66 RPM
bodymap2_kidney	0.27 RPM	2.90 RPM
bodymap2_liver	0.00 RPM	0.06 RPM
bodymap2_lung	0.04 RPM	1.72 RPM
bodymap2_lymph_node	1.17 RPM	3.82 RPM
bodymap2_ovary	1.08 RPM	0.56 RPM
bodymap2_prostate	1.14 RPM	0.31 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.16 RPM
bodymap2_testis	0.57 RPM	36.69 RPM
bodymap2_thyroid	0.15 RPM	1.47 RPM
bodymap2_white_blood_cells	0.02 RPM	0.96 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4187 was not detected

EST

1 EST(s) were mapped to retro_hsap_4187 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CR747078	89627104	89627632	99.9	524	1	522

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_194554	645 libraries	289 libraries	680 libraries	170 libraries	45 libraries

The graphical summary, for retro_hsap_4187 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_4187 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4187 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2843
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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	2.25 RPM
CEU_NA11843	1.34 RPM
CEU_NA11930	0.10 RPM
CEU_NA12004	0.11 RPM
CEU_NA12400	2.39 RPM
CEU_NA12751	1.58 RPM
CEU_NA12760	0.13 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	2.56 RPM
CEU_NA12873	2.14 RPM
FIN_HG00183	1.18 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.06 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	3.01 RPM
FIN_HG00338	1.92 RPM
FIN_HG00349	2.50 RPM
FIN_HG00375	0.07 RPM
FIN_HG00377	0.10 RPM
FIN_HG00378	2.15 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.04 RPM
GBR_HG00114	0.08 RPM
GBR_HG00119	1.27 RPM
GBR_HG00131	1.49 RPM
GBR_HG00133	1.57 RPM
GBR_HG00134	1.64 RPM
GBR_HG00137	1.26 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	3.10 RPM
TSI_NA20512	2.60 RPM
TSI_NA20513	2.32 RPM
TSI_NA20518	1.39 RPM
TSI_NA20532	1.94 RPM
TSI_NA20538	1.89 RPM
TSI_NA20756	0.06 RPM
TSI_NA20765	2.69 RPM
TSI_NA20771	0.11 RPM
TSI_NA20786	5.81 RPM
TSI_NA20798	0.09 RPM
YRI_NA18870	2.57 RPM
YRI_NA18907	2.11 RPM
YRI_NA18916	1.77 RPM
YRI_NA19093	2.76 RPM
YRI_NA19099	0.08 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.06 RPM
YRI_NA19213	0.12 RPM
YRI_NA19214	0.07 RPM
YRI_NA19223	3.18 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).