RetrogeneDB ID: retro_mmul_1467

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:137152393..137152891(+)
• Located in intron of: ENSMMUG00000017699

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAP30
• Ensembl ID: ENSMMUG00000002401
• Aliases: None
• Description: histone deacetylase complex subunit SAP30 [Source:RefSeq peptide;Acc:NP_001253261]

Sequence

>retro_mmul_1467
GCTGGGCCCCCGGGGGCGGCCAGGCCAGGCTCCGGACAACTGTGCTGCCTGCGGAGGATGGTGAGCAGTGCGGCCGGGCG
GCAGGCAACGCCAGCTTCAGCAAGAGGATCCAGAGGAGCATATCCCAGAAGGTGAAGATCGAGCTGGATATGAGCGCAGG
CATCTTTACATATGTGATTATCATAAAAACTTAATTCAGAGTATTCGAAACAGAAGAAAGAGAAAAGGGAGTGATGACGA
TGGAGGTGATTCACCTGTTCAAGATATTGATACCCCAGAGGTTGATTTATACCAATTACAAGTAAATACACTTAGGAGAT
ACAAAAGACACTTAAAGCCAGCAACCAACCAGGACTTAATAAAGCACAACTTGTTGAGATAGTTGGTTGCCACTTTAGGT
CTATTCCAGTGAGTGAAAAAGACATCTTAACATATTTCATCTAATCAGTGAAGAATGACAAGAACAAATCAGATCTCAAG
GTTGACAGTGGTGTTCAT

Alignment

ORF - retro_mmul_1467 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.47 %
• Parental protein coverage: 76.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AGPPGAAGPGPGQLCCLR-EDGERCGRAAGNASFSKRIQKSISQKKVKIELDKSA-RHLYICDYHKNLIQ
          AGPPGAA.PG.GQLCCLR.EDGE.CGRAAGNASFSKRIQ.SISQK.VKIELD.SA.RHLYICDYHKNLIQ
Retrocopy AGPPGAARPGSGQLCCLR<EDGEQCGRAAGNASFSKRIQRSISQK-VKIELDMSA<RHLYICDYHKNLIQ

Parental  SVRNRRKRKGSDDDGGDSPVQDIDTPEVDLYQLQVNTLRRYKRHFKLPT-RPGLNKAQLVEIVGCHFRSI
          S.RNRRKRKGSDDDGGDSPVQDIDTPEVDLYQLQVNTLRRYKRH.K..T..PGLNKAQLVEIVGCHFRSI
Retrocopy SIRNRRKRKGSDDDGGDSPVQDIDTPEVDLYQLQVNTLRRYKRHLKPAT<QPGLNKAQLVEIVGCHFRSI

Parental  PVNEKDTLTYFIYSVKNDKNKSDVKVDSGVH
          PV.EKD.LTYFI.SVKNDKNKSD.KVDSGVH
Retrocopy PVSEKDILTYFI*SVKNDKNKSDLKVDSGVH

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	0.00 RPM	4.59 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	3.09 RPM
SRP007412_cerebellum	0.00 RPM	7.56 RPM
SRP007412_heart	0.00 RPM	3.36 RPM
SRP007412_kidney	0.00 RPM	1.64 RPM
SRP007412_liver	0.00 RPM	0.99 RPM
SRP007412_testis	0.11 RPM	8.71 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1467 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1467 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1467 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2864
Pan troglodytes	retro_ptro_1936
Gorilla gorilla	retro_ggor_1980

---

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,