RetrogeneDB ID: retro_ptro_3093

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:22081018..22081807(+)
• Located in intron of: ENSPTRG00000021735

Retrocopy information

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

Parental gene information

• Parental gene symbol: YY1
• Ensembl ID: ENSPTRG00000006717
• Aliases: None
• Description: YY1 transcription factor [Source:UniProtKB/TrEMBL;Acc:K7DAI9]

Sequence

>retro_ptro_3093
GATAGCATTGAAGACGAGCACTTCCAGATGACCCTGGCCTCTCTGTCGGCCTCGGCGGCATCAACATCAACATCAACCCA
GAGCCGCAGCAAAAAGCCCAGCAAAAAGCCCAGCGGCAAGAGTGCCACCAGCACTGAGGCCAACCCGGCAGGCAGCAGCT
CCAGCGAGGGCACGAGGAAGTGGGAGCAGAAGCAAATGCAGGTCAAAACGCTGGAGGGTGAGTTTTCCGTGACTATGTGG
TCCCCTAACGATAACAATGACCAAGGGGCAGTGGGTGAAGGCCAGGCTGAAAACCCACCTGATTATTCCGAGTACTTGAA
AGGGAAGAAACTTCCTCCTGGGGGGTTACCAGGCGTCGATCTCTCAGATCCTAAACAGCTGGCAGAATTTACTAAAGTGA
AGCCCAAAAGGTCCAAAGGAGAACCTCCCAAAACAGTCGCTTGCTCTTATAGCGGCTGCGAAAAGATGTTCCGGGATTAC
GCCGCCATGAGAAAACATCTCCACATCCACGGGCCCAGAGTCCACGTATGCACAGAATGTGGCAAAGCTTTTCTTGAGAG
CTCAAAGCTGAGACGACACCAGCTGGTCCACACCGGCGAGAAGCCCTTTCAGTGCACATTCGAAGGCTGCGGGAAACGCT
TTTCCCTTGATTTCAATTTGCGCACACACTTGCGCATCCACACCGGCGATAAGCCCTTCGTGTGCCCCTTCGATGTTTGC
AACAGGAAGTTCGCTCAGTCAACCAACCTGAAAACCCACATATTAACGCATGTGAAGACCAAAAACAAC

Alignment

ORF - retro_ptro_3093 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.96 %
• Parental protein coverage: 83.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DYIEQTLVTVAAAGKSGGGGSSSSGGGRVKKGGGKKSGKKSYLSGGAGAAGGGGADPGNKKWEQKQVQIK
          D.IE........A..S....S.S................KS..S..A..AG......G..KWEQKQ.Q.K
Retrocopy DSIEDEHFQMTLASLSASAASTSTSTQXXXXXXXXXXXGKSATSTEANPAGSSSSE-GTRKWEQKQMQVK

Parental  TLEGEFSVTMWSSDEKKDIDHETVVEEQIIGENSPPDYSEYMTGKKLPPGGIPGIDLSDPKQLAEFARMK
          TLEGEFSVTMWS.......D...V.E.Q......PPDYSEY..GKKLPPGG.PG.DLSDPKQLAEF...K
Retrocopy TLEGEFSVTMWSPNDNN--DQGAVGEGQA---ENPPDYSEYLKGKKLPPGGLPGVDLSDPKQLAEFTKVK

Parental  PRKIKEDDAPRTIACPHKGCTKMFRDNSAMRKHLHTHGPRVHVCAECGKAFVESSKLKRHQLVHTGEKPF
          P...K....P.T.AC...GC.KMFRD..AMRKHLH.HGPRVHVC.ECGKAF.ESSKL.RHQLVHTGEKPF
Retrocopy PKRSK-GEPPKTVACSYSGCEKMFRDYAAMRKHLHIHGPRVHVCTECGKAFLESSKLRRHQLVHTGEKPF

Parental  QCTFEGCGKRFSLDFNLRTHVRIHTGDRPYVCPFDGCNKKFAQSTNLKSHILTHAKAKNN
          QCTFEGCGKRFSLDFNLRTH.RIHTGD.P.VCPFD.CN.KFAQSTNLK.HILTH.K.KNN
Retrocopy QCTFEGCGKRFSLDFNLRTHLRIHTGDKPFVCPFDVCNRKFAQSTNLKTHILTHVKTKNN

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	0.20 RPM	11.55 RPM
SRP007412_cerebellum	1.04 RPM	16.02 RPM
SRP007412_heart	0.15 RPM	10.61 RPM
SRP007412_kidney	0.18 RPM	20.11 RPM
SRP007412_liver	0.29 RPM	16.27 RPM
SRP007412_testis	1.90 RPM	21.92 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3093 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3093 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3093 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3616

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011146	1 retrocopy	retro_amel_2,
Callithrix jacchus	ENSCJAG00000016853	2 retrocopies	retro_cjac_1931, retro_cjac_4045,
Equus caballus	ENSECAG00000005805	1 retrocopy	retro_ecab_97,
Homo sapiens	ENSG00000100811	2 retrocopies	retro_hsap_106, retro_hsap_97,
Gorilla gorilla	ENSGGOG00000026332	2 retrocopies	retro_ggor_190, retro_ggor_2,
Mus musculus	ENSMUSG00000021264	1 retrocopy	retro_mmus_190,
Nomascus leucogenys	ENSNLEG00000000999	3 retrocopies	retro_nleu_1092, retro_nleu_116, retro_nleu_2225,
Otolemur garnettii	ENSOGAG00000006955	4 retrocopies	retro_ogar_1231, retro_ogar_1804, retro_ogar_1857, retro_ogar_289,
Pongo abelii	ENSPPYG00000025949	3 retrocopies	retro_pabe_145, retro_pabe_3616, retro_pabe_534,
Pan troglodytes	ENSPTRG00000006717	3 retrocopies	retro_ptro_3093 , retro_ptro_45, retro_ptro_494,