RetrogeneDB ID: retro_pabe_3616

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:21908619..21909120(+)
• Located in intron of: ENSPPYG00000020181

Retrocopy information

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

Parental gene information

• Parental gene symbol: YY1
• Ensembl ID: ENSPPYG00000025949
• Aliases: None
• Description: YY1 transcription factor [Source:HGNC Symbol;Acc:12856]

Sequence

>retro_pabe_3616
GAAAACTCACCTGATTATTCCGAGTACTTGAAAGGGAAGAAACTTCCTCCTGAGGGGTTACCAGGCATTGATCTCTCAGA
TCCTAAACAGCTGGCAGAATTTACTAAAGTGAAGCCCAAAAGGTCCAAAGGAGAACCTCCCAAAACAGTCCCTTGTTCTC
ATAGCGGCTGCGAAAAGATGTTCAGGGATTACTCCTCCATGAGAAAACATCTCCACATCCATGGGCCCAGAGTCCACGTA
TGTGCAGAATGTGGCAAAGCTTTTCTTGAGAGCTCAAAGCTGAAACGACACCAGCTGGTCCACACCGGCGAGAAGCCGTT
TCAGTGCACATTCGAAGGCTGCGGGAAACGCTTTTCCCTTGATTTCAATTTGCGCACACACTTGCGCATCCACACCGGCG
ATAAGCCCTTCGTGTGCCCCTTCGATGTTTGCAACAGGAGGTTCGCTCAGTCAACCAACCTGAAAACCCACATATTAACG
CATGTAAAGAACAAAAACAGC

Alignment

ORF - retro_pabe_3616 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.29 %
• Parental protein coverage: 89.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ENSPPDYSEYMTGKKLPPGGIPGIDLSDPKQLAEFARMKPRKIKEDDAPRTIACPHKGCTKMFRDNSAMR
          ENSP.DYSEY..GKKLPP.G.PGIDLSDPKQLAEF...KP...K....P.T..C.H.GC.KMFRD.S.MR
Retrocopy ENSP-DYSEYLKGKKLPPEGLPGIDLSDPKQLAEFTKVKPKRSK-GEPPKTVPCSHSGCEKMFRDYSSMR

Parental  KHLHTHGPRVHVCAECGKAFVESSKLKRHQLVHTGEKPFQCTFEGCGKRFSLDFNLRTHVRIHTGDRPYV
          KHLH.HGPRVHVCAECGKAF.ESSKLKRHQLVHTGEKPFQCTFEGCGKRFSLDFNLRTH.RIHTGD.P.V
Retrocopy KHLHIHGPRVHVCAECGKAFLESSKLKRHQLVHTGEKPFQCTFEGCGKRFSLDFNLRTHLRIHTGDKPFV

Parental  CPFDGCNKKFAQSTNLKSHILTHAKAKNN
          CPFD.CN..FAQSTNLK.HILTH.K.KN.
Retrocopy CPFDVCNRRFAQSTNLKTHILTHVKNKNS

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	0.39 RPM	8.79 RPM
SRP007412_cerebellum	1.70 RPM	19.09 RPM
SRP007412_heart	0.33 RPM	5.72 RPM
SRP007412_kidney	0.27 RPM	9.78 RPM
SRP007412_liver	0.34 RPM	9.61 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3616 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3616 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3616 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_3093

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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,