RetrogeneDB ID: retro_cjac_1608

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:63609369..63610859(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC20
• Ensembl ID: ENSCJAG00000003414
• Aliases: None
• Description: None

Sequence

>retro_cjac_1608
ATGGCTCAGTTAGCATTTGAGAGTGACCTGCACTCGCTGCTTCAGCTGGATACACCCATCCCCAGTGCACCCCCTGCGCG
CTGGCAGCGCAAAGCCAAGGAAGCCGCAGGCCTGGCCGCCTCACCCATGCGGGCCGCCAACTGATCCCACAGCGCTGGCA
GGACTCCGGGCTGAACTCCTGGCAAATCCAGTTCCAAGGTTCAGACCACTCCTAGCAAACCTGGCGGTGACCGCTATATC
CCCCAACGCAGTGCTGCCCAGATGGAGGTGGCCAGCTTCCTCCTGAGCAAGGAGAACGAGCCTGAAAACAGCCAGACGCC
CACCAAGAAGGAACATCAGAAAGCCTGGGCTTTGAACCTGAACAGTTTTGATGTAGAGGAAGTCAAGATCCTTCGGCTCA
GTGGAAAACCACAAACTGCCCCAGAGGGTTACCAGAACAGACTGAAAGTACTCTACAGTCAAAAGGCCACGCCTGGCTCC
AGCCGGAAGACCTGCCGTTACATTCCTTCCCTGCCAGATCGTATCCTAGATGCCCCAGAAATCCGAAATGACTACTACCT
GAAACTTGTGGATTGGAGCTCTGGGAATGTCCAGGCTGTGGCACTGGACAACAGTGTGTACCTGTGGAGTGCAAGCTCTG
GTGACATCCTGCAGCTTTTGCAAATGGAGCAGCCTGGGGAATATGTATCCTCTGTGGCCTGGATCAAAGAGGGCAACTAC
TTGGCTGTGGGCACCAGCAGTGCTGATGTGCAGCAATGGGATGTGCAGCAGCAGAAACGGCTTCGAAATGACCAGTCACT
CTGCCCGAGTGAGCTCCCTAAGTTGGAACAGCTATATCCTGTCCAGTGGATCACGTTCTGGCCATATCCACCACCATGAT
GTTCAGGTAGCAGAACACCATGTGGCCACACTGAGTGGCCACAGCCAGGAAGTATGTGGGCTGCGCTGGGCCCCAGATGG
ATGACATTTGGCCAGTGCTGGCAATAACTTGGTCAATGTGTGGCCTAGTGCTCCTGGAGAGGGTGGCTGGGTTCCTCTGC
GAACATTCACCCAGCATCAAGGGGCTGTCAAGGCTGTAGCATGGTGTCCCTGGCAGTCCAATGTCCTGGCAACAGGAGGA
GGCACCAGTGATCGACACATTCGCATCTGGAATGTGTGCTCTGGGGCCTGTCTGAGTGCTGTGGATGCCCATTCCCAGGT
GTGCTCCATCCTCTGGTCTCCCCACTACAAGGAGCTCATCTCAGGCCACGGCTTTTCACAGAACCAGCTGGTTATTTGGA
AGTACCCAACCATGGAAAGGTGGCTGAACTGAAAGGTCACACATCCCGGGTCCTGAGTCTGACCATGAGCCCAGATGGGG
CCACAGTGGCATCTGCAGCAGCAGATGAGACCCTGAGGCTATGGCGCTGTTTGAGTTGGACCCTGCATGGCGGCGGGAGT
GGGAGAAGGCCAATGCAGCCAAAAGCAGCCTCATCCACCAAGGCATCCGC

Alignment

ORF - retro_cjac_1608 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.43 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAQFAFESDLHSLLQLDTPIPNAPPARWQRKAKEAAGPAPSPMRAANRSHSAGRTPGRTPGKSSSKVQTT
          MAQ.AFESDLHSLLQLDTPIP.APPARWQRKAKEAAG.A.SPMRAAN.SHSAGRTPG.TPGKSSSKVQTT
Retrocopy MAQLAFESDLHSLLQLDTPIPSAPPARWQRKAKEAAGLAASPMRAAN*SHSAGRTPG*TPGKSSSKVQTT

Parental  PSKPGGDRYIPQRSAAQMEVASFLLSKENQPENSQTPTKKEYQKAWALNLNGFDVEEAKILRLSGKPQNA
          PSKPGGDRYIPQRSAAQMEVASFLLSKEN.PENSQTPTKKE.QKAWALNLN.FDVEE.KILRLSGKPQ.A
Retrocopy PSKPGGDRYIPQRSAAQMEVASFLLSKENEPENSQTPTKKEHQKAWALNLNSFDVEEVKILRLSGKPQTA

Parental  PEGYQNRLKVLYSQKATPGSSRKTCRYIPSLPDRILDAPEIRNDYYLNLVDWSSGNVLAVALDNSVYLWS
          PEGYQNRLKVLYSQKATPGSSRKTCRYIPSLPDRILDAPEIRNDYYL.LVDWSSGNV.AVALDNSVYLWS
Retrocopy PEGYQNRLKVLYSQKATPGSSRKTCRYIPSLPDRILDAPEIRNDYYLKLVDWSSGNVQAVALDNSVYLWS

Parental  ASSGDILQLLQMEQPGEYVSSVAWIKEGNYLAVGTSSAEVQLWDVQQQKRLRN-MTSHSARVGSLSWNSY
          ASSGDILQLLQMEQPGEYVSSVAWIKEGNYLAVGTSSA.VQ.WDV.QQ......MTSHSARV.SLSWNSY
Retrocopy ASSGDILQLLQMEQPGEYVSSVAWIKEGNYLAVGTSSADVQQWDV-QQQKRLR>MTSHSARVSSLSWNSY

Parental  ILSSGSRSGHIHHHDVRVAEHHVATLSGHSQEVCGLRWAPDGRHLASGGNDNLVNVWPSAPGEGGWVPLQ
          ILSSGSRSGHIHHHDV.VAEHHVATLSGHSQEVCGLRWAPDG.HLAS.GN.NLVNVWPSAPGEGGWVPL.
Retrocopy ILSSGSRSGHIHHHDVQVAEHHVATLSGHSQEVCGLRWAPDG*HLASAGN-NLVNVWPSAPGEGGWVPLR

Parental  TFTQHQGAVKAVAWCPWQSNVLATGGGTSDRHIRIWNVCSGACLSAVDAHSQVCSILWSPHYKELISGHG
          TFTQHQGAVKAVAWCPWQSNVLATGGGTSDRHIRIWNVCSGACLSAVDAHSQVCSILWSPHYKELISGHG
Retrocopy TFTQHQGAVKAVAWCPWQSNVLATGGGTSDRHIRIWNVCSGACLSAVDAHSQVCSILWSPHYKELISGHG

Parental  FSQNQLVIWKYPTM-AKVAELKGHTSRVLSLTMSPDGATVASAAADETLRLWRC-FELDPARRREREKAN
          FSQNQLVIWKYPTM..KVAELKGHTSRVLSLTMSPDGATVASAAADETLRLWRC.FELDPA.RRE.EKAN
Retrocopy FSQNQLVIWKYPTM<GKVAELKGHTSRVLSLTMSPDGATVASAAADETLRLWRC<FELDPAWRREWEKAN

Parental  AAKSSLIHQGIR
          AAKSSLIHQGIR
Retrocopy AAKSSLIHQGIR

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
SRP051959_colon	0.02 RPM	20.39 RPM
SRP051959_heart	0.02 RPM	0.86 RPM
SRP051959_kidney	0.04 RPM	0.82 RPM
SRP051959_liver	0.00 RPM	0.50 RPM
SRP051959_lung	0.03 RPM	2.39 RPM
SRP051959_lymph_node	0.00 RPM	5.05 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.46 RPM
SRP051959_spleen	0.00 RPM	4.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1608 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1608 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1608 has 0 orthologous retrocopies within eutheria group .

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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,