RetrogeneDB ID: retro_pabe_622

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:98700073..98700414(-)
• Located in intron of: ENSPPYG00000002555

Retrocopy information

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

Parental gene information

• Parental gene symbol: EBAG9
• Ensembl ID: ENSPPYG00000018824
• Aliases: None
• Description: estrogen receptor binding site associated, antigen, 9 [Source:HGNC Symbol;Acc:3123]

Sequence

>retro_pabe_622
ATGGCCATAACACAGGTCCAGTTATTTCGAGTTTATACTTGCCTAGCAACCGTATTCTCATTCCTCAAAAGGATAAGTAT
GAAGATCTGTCCAAGGACAGAAATTAAGTTGGGTCCAAGTAACTTTGCCAATTGCAGTTAATTATTCATCAGTTCCTAAA
CAGACAGATGTTGAAGAGTGGACTTCTTAGAATGAGGATGCACCCGCAAGTGTAAAGACCGAGGGTGAGAATGGAATGAG
GCAGTGCAACCGAACACTTTACAACAACTGGAACCGACTATTTTAAGGATGTGACACCAACTGTAAGGAAAACTCAGAAA
ATTGTTATTGAGAAGAGACAA

Alignment

ORF - retro_pabe_622 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.94 %
• Parental protein coverage: 53.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAITQFRLFKFCTCLATVFSFLKRL-ICRSGRGRKLSGDQITLPTTVDYSSVPKQTDVEEWTSWDEDAPT
          MAITQ..LF...TCLATVFSFLKR....RS..G.KLS..Q.TLP..V.YSSVPKQTDVEEWTS..EDAP.
Retrocopy MAITQVQLFRVYTCLATVFSFLKRI>V*RSVQGQKLSWVQVTLPIAVNYSSVPKQTDVEEWTS*NEDAPA

Parental  SVKIEGGNG-NVATQQNSLEQLEP-DYFKDMTPTIRKTQKIVIKKRE
          SVK.EG.NG.N.A.Q.N.L.QLEP.DYFKD.TPT.RKTQKIVI.KR.
Retrocopy SVKTEGENG<NEAVQPNTLQQLEP<DYFKDVTPTVRKTQKIVIEKRQ

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	0.06 RPM	16.53 RPM
SRP007412_cerebellum	0.00 RPM	23.10 RPM
SRP007412_heart	0.00 RPM	7.71 RPM
SRP007412_kidney	0.03 RPM	16.67 RPM
SRP007412_liver	0.03 RPM	13.22 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_622 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_622 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_622 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_515

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000007465	2 retrocopies	retro_dnov_1014, retro_dnov_2449,
Macropus eugenii	ENSMEUG00000014115	3 retrocopies	retro_meug_1871, retro_meug_2058, retro_meug_597,
Monodelphis domestica	ENSMODG00000004795	2 retrocopies	retro_mdom_261, retro_mdom_665,
Pongo abelii	ENSPPYG00000018824	1 retrocopy	retro_pabe_622 ,
Pan troglodytes	ENSPTRG00000020513	1 retrocopy	retro_ptro_515,