RetrogeneDB ID: retro_pabe_2366

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:153476000..153476531(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAP30
• Ensembl ID: ENSPPYG00000015205
• Aliases: None
• Description: Sin3A-associated protein, 30kDa [Source:HGNC Symbol;Acc:10532]

Sequence

>retro_pabe_2366
GGGGCTGAGGGGCCGGGCGCAGGGGCGGTCTCAGCGGCTGGGCCCCCGGGGGCGGCCAGGCCGGGCTCCTGGCAACTGTG
CTGCCTGCGGACGACGGTGAGCGGTGCGGTCGGGCGGCAGGCAACGCCAGCTTCAGCAAGAGGATCCAGAAGAGGATATC
CCAGAAGGTGAAGATCGAGCTGGATAAGAGCGCAGGCATCTTTACATATGTGATTATCATAAAAACTTAATTCAGAGTAT
TCGAAACAGAAGAGAAAAGGGAGTGATGATGATGGAGGTGATACACCTGTTCAAGATTTTGATACCCCAGAGGTTGATTT
ATACCAATTACAAGTAAATACACTTAGGAGATACAAAAGACACTTAAAGCCACCAACCAGACCAGGACTTAATAAAGCAC
AACTTGTTGAGATAGTTGGTTGCCACTTTAGGTCTATTCCAGTGAGTGAAAAAGACACCTTAACATATTTCAACTGATCA
GTGAAGAATAACAAGAACAAATCAGATCTCAAGGTTGATAGTGGTGTTCAC

Alignment

ORF - retro_pabe_2366 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.98 %
• Parental protein coverage: 90.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GAEVPGAGAVSAAGPPGAAGPGPGQLCCLR-EDGERCGRAAGNASFSKRIQKSISQKKVKIELDKSA-RH
          GAE.PGAGAVSAAGPPGAA.PG..QLCCLR..DGERCGRAAGNASFSKRIQK.ISQ.KVKIELDKSA.RH
Retrocopy GAEGPGAGAVSAAGPPGAARPGSWQLCCLR<DDGERCGRAAGNASFSKRIQKRISQ-KVKIELDKSA<RH

Parental  LYICDYHKNLIQSVRNRRKRKG-SDDDGGDSPVQDIDTPEVDLYQLQVNTLRRYKRHFKLPTRPGLNKAQ
          LYICDYHKNLIQS.RNRR..KG.SDDDGGD.PVQD.DTPEVDLYQLQVNTLRRYKRH.K.PTRPGLNKAQ
Retrocopy LYICDYHKNLIQSIRNRRE-KG<SDDDGGDTPVQDFDTPEVDLYQLQVNTLRRYKRHLKPPTRPGLNKAQ

Parental  LVEIVGCHFRSIPVNEKDTLMYFIYSVKNDKNKSDLKVDSGVH
          LVEIVGCHFRSIPV.EKDTL.YF..SVKN.KNKSDLKVDSGVH
Retrocopy LVEIVGCHFRSIPVSEKDTLTYFN*SVKNNKNKSDLKVDSGVH

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	7.57 RPM
SRP007412_cerebellum	0.12 RPM	6.57 RPM
SRP007412_heart	0.06 RPM	2.14 RPM
SRP007412_kidney	0.17 RPM	2.29 RPM
SRP007412_liver	0.15 RPM	1.13 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2366 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2366 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2366 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000164105	1 retrocopy	retro_hsap_2864,
Gorilla gorilla	ENSGGOG00000005082	2 retrocopies	retro_ggor_1980, retro_ggor_3072,
Macaca mulatta	ENSMMUG00000002401	1 retrocopy	retro_mmul_1467,
Monodelphis domestica	ENSMODG00000003536	1 retrocopy	retro_mdom_608,
Nomascus leucogenys	ENSNLEG00000006666	1 retrocopy	retro_nleu_605,
Pongo abelii	ENSPPYG00000015205	1 retrocopy	retro_pabe_2366 ,
Pan troglodytes	ENSPTRG00000016598	1 retrocopy	retro_ptro_1936,