RetrogeneDB ID: retro_pabe_534

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:64793821..64794309(+)
• Located in intron of: ENSPPYG00000002369

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_534
GACTTTGATACTTCAACAGTAGTTGAAGAACTGGCCATTGAAGAGAACCTGCCTCCTGATTTTCAGAGTATATGACAGGA
AAGAAACTTCCTCCTGGAGGAATACCTGGCAGTAACCTCTCAAATCCTAAACAATGGGCATAACTTGCTAGAATGAAGCC
AAGAAAAATTAAATAAGGTGATGCTCCAAGAACAACAGCTTGCCCTCATAAAGGGAGCACAAAGATGTTCTTGGATAACT
CTGCCATGAGAAAACATCTATACAGCCACAGTCCCAGAGTCCTCGTTTGTGAAGAACATGGCAAAGCTCTTGCTGAGAGC
TCAAGACCAGAACAACACCAAGCAGTCCGTGCTGGAGAGAAGCTCTTTCATGTCACATGGTGGGTCTGCGGGAAACGCTT
TTTATTGGACTTCAATTTGTGCACACATGTGTGAATCCATACCAGAGACAGGACCCATGTGTGCCCCTTCCGTGGTTGTA
ATAAAAGA

Alignment

ORF - retro_pabe_534 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.12 %
• Parental protein coverage: 86.24 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DIDHETVVEEQIIGENSPPDY-SEYMTGKKLPPGGIPGIDLSDPKQLAEFARMKPRKIKEDDAPRTIACP
          D.D..TVVEE..I.EN.PPD..SEYMTGKKLPPGGIPG..LS.PKQ.A..ARMKPRKIK..DAPRT.ACP
Retrocopy DFDTSTVVEELAIEENLPPDF<SEYMTGKKLPPGGIPGSNLSNPKQWA*LARMKPRKIK*GDAPRTTACP

Parental  HKGCTKMFRDNSAMRKHLHTHGPRVHVCAECGKAFVESSKLKRHQLVHTGEKPFQCTFEGCGKRFSLDFN
          HKG.TKMF.DNSAMRKHL..H.PRV.VC.E.GKA..ESS....HQ.V..GEK.F..T...CGKRF.LDFN
Retrocopy HKGSTKMFLDNSAMRKHLYSHSPRVLVCEEHGKALAESSRPEQHQAVRAGEKLFHVTWWVCGKRFLLDFN

Parental  LRTHVRIHTGDRPYVCPFDGCNKK
          L.THV.IHT.DR..VCPF.GCNK.
Retrocopy LCTHV*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	8.79 RPM
SRP007412_cerebellum	0.00 RPM	19.09 RPM
SRP007412_heart	0.00 RPM	5.72 RPM
SRP007412_kidney	0.07 RPM	9.78 RPM
SRP007412_liver	0.03 RPM	9.61 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_534 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_534 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_534 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_494

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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,