RetrogeneDB ID: retro_ptro_494

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:68992631..68993245(-)
• Located in intron of: None

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_494
GGTGGTGATGGCGCCAACCCACGCAACAACAAGTGGGAGCAGAAGCAGGTGCAGATCAAGAACCTGGAGGGCAAGTTTTT
GGTCACCATGTAGTCCTCAGAGAAAAAAAAAAAAAAAAAAGATATTGACTTTGATACTTCAACAGTGGTTGAAGAACTGG
CCATTGAAGAGAACCTGCCTCCTGATTTTCAGAGTATATGACAGGAAAGAAACTTCCTCCTGGAGGAATACCTGGCAGTA
ACCTCTCAAATCCTAAACAATTGGCATAACTTGCTAGACTGAAGCCAAGAAAAATTAAATAAGATGATGCCCCAAGAACA
ACAGCTTGCCCTCATAAAGGGAGCACGAAGATGTTCTTGGATAACTCTGCCATGAGAAAACATCTGCACAGCCACAGTCC
CAGAGTCCTCGTCTGTGAAGAACACGGCAAAGCTCTTGTTGAGAGCTCAAGACCAGAACAACACCAACCAGTCTGTGCTG
GAGAGAAGCTCTTTCATGGCACATGGTGGGTCTGTGGGAAATGCTTTTTATTGGACTTCAATTTGTGCACGCGTGTGTGA
ATCCATACCAGAGACAGGACCCATGTGTGCCCCTTCCGTGGTTGTAATAAAAGA

Alignment

ORF - retro_ptro_494 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.93 %
• Parental protein coverage: 61.54 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGGGADPGNKKWEQKQVQIKTLEGEFSVTMWSSD---EKKDIDHE--TVVEEQIIGENSPPD-YSEYMTG
          GG.GA.P.N.KWEQKQVQIK.LEG.F.VTM.SS.......DID....TVVEE..I.EN.PPD..SEYMTG
Retrocopy GGDGANPRNNKWEQKQVQIKNLEGKFLVTM*SSEXXXXXXDIDFDTSTVVEELAIEENLPPD<FSEYMTG

Parental  KKLPPGGIPGIDLSDPKQLAEFARMKPRKIKEDDAPRTIACPHKGCTKMFRDNSAMRKHLHTHGPRVHVC
          KKLPPGGIPG..LS.PKQLA..AR.KPRKIK.DDAPRT.ACPHKG.TKMF.DNSAMRKHLH.H.PRV.VC
Retrocopy KKLPPGGIPGSNLSNPKQLA*LARLKPRKIK*DDAPRTTACPHKGSTKMFLDNSAMRKHLHSHSPRVLVC

Parental  AECGKAFVESSKLKRHQLVHTGEKPFQCTFEGCGKRFSLDFNLRTHVRIHTGDRPYVCPFDGCNKK
          .E.GKA.VESS....HQ.V..GEK.F..T...CGK.F.LDFNL.T.V.IHT.DR..VCPF.GCNK.
Retrocopy EEHGKALVESSRPEQHQPVCAGEKLFHGTWWVCGKCFLLDFNLCTRV*IHTRDRTHVCPFRGCNKR

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	0.00 RPM	11.55 RPM
SRP007412_cerebellum	0.00 RPM	16.02 RPM
SRP007412_heart	0.00 RPM	10.61 RPM
SRP007412_kidney	0.00 RPM	20.11 RPM
SRP007412_liver	0.00 RPM	16.27 RPM
SRP007412_testis	0.11 RPM	21.92 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_494 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_494 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_494 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_534

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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 ,