RetrogeneDB ID: retro_mmul_1884

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:60280894..60281887(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPOPL
• Ensembl ID: ENSMMUG00000002560
• Aliases: None
• Description: speckle-type POZ protein-like [Source:RefSeq peptide;Acc:NP_001253311]

Sequence

>retro_mmul_1884
CAGGAATCCGCCCCACCTCTACACAGAAATATGTCTTCTTTTCCCATAGCAGAAAGCTAGTGTTATACACAGGTCAAAAT
AGTAAAATGTTCAACACATAGACCATTAACAACTTCAGTTTTTGTCAAGAGGAAATGGGTGACGTGGTAAAAAGTTCAAC
ATTTTCACTCGGCCCAGTGACGAAATGGTGACTGAGGGTAAACCCAAAGGGATTAGATAATGAAAGTAAAGAAAACTTGT
TCCTATATTTGCTTTTAGTCAGGTGCCCCAAAAGTGAAGTAGGAGCAAAATTCAAATTTTCCCTTCTGAATGCCAAAAGG
GAAGAAACAAAAGCAATGGAAAGCCAAAGAGCATATCAATTCATTCAAGGGAAGGACTAAGATTTTAAAAATTATTTAGA
GGGGACATTTAGCTTGACAAAGCTAATGGTCTTCTACCAGATAACAAGCTCACATTATTTTGTGAGGTGAGTGTGGTCCA
AGATTCAATAAACAAATCAGGACATACTAATACAAATACTTTGAAGGTGGCTGAGTGTCAGCTAGGAGAAGATGTAGGTA
ATCTCGGGGAAACACAGTATTTACAGACTGCAGTTTTTTGTGACAGGACAAGAATTTAAAGCTCACAAATCTGCTTGTAC
CTCCATCTCCTGTTTTTAGTGCCATGTTTGAACATGAAATGGAAGAAAGCATAAAGAATCGAGTGGAGATAAATGATTTA
GACCCTGATGTTTTTAAAGAAATGATGAGATTCAATAACACAAGGAAATAAGTAAACCTTGACAAAATGGCTGACAACTT
GTGGGCAGCTGCAGGCAAACATGCACTGGGAACAGTTGAAGGTGATGTGTGAGGAAGTTTTGTGTAGCAATACCTCAGTA
GAAAATGTTGCTGATACCCTTGTCCTTGCAGATTTGCACATTGCGGAACAGTTGGAAGCACAAGCATAGACATTATTAAT
AGTTGCATTGTACTTTGACAACTTGGATGTAAA

Alignment

ORF - retro_mmul_1884 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.94 %
• Parental protein coverage: 85.46 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  REPTPPLPGDMSTGPIAESWCYTQVKVV-KFSYMWTINNFSFCREEMGEVLKSSTFSSGPSDKMKWCLRV
          .E..PPL...MS..PIAES.CYTQVK.V.K.....TINNFSFC.EEMG.V.KSSTFS.GP..K..W.LRV
Retrocopy QESAPPLHRNMSSFPIAES*CYTQVKIV<KMFNT*TINNFSFCQEEMGDVVKSSTFSLGPVTK--W*LRV

Parental  NPKGLDDESKDYLSLYLLLVSCPKSEVRAKFKFSLLNAKREETKAMESQRAYRFVQGKDWGFKKFI-RRD
          NPKGLD.ESK..L.LYLLLV.CPKSEV.AKFKFSLLNAKREETKAMESQRAY.F.QGKD..FK....R.D
Retrocopy NPKGLDNESKENLFLYLLLVRCPKSEVGAKFKFSLLNAKREETKAMESQRAYQFIQGKD*DFKNYL<RGD

Parental  FLLDEANGLLPDDKLTLFCEVSVVQDSVNISGHTNTNTLKVPECRLAEDLGNLWE-NTRFTDCSFFVRGQ
          ..LD.ANGLLPD.KLTLFCEVSVVQDS.N.SGHTNTNTLKV.EC.L.ED.GNL.E.NT.FTDCSF.....
Retrocopy I*LDKANGLLPDNKLTLFCEVSVVQDSINKSGHTNTNTLKVAECQLGEDVGNLGE<NTVFTDCSFL*QDK

Parental  EFKAHKSVLAARSPVFNAMFEHEMEESKKNQVEINDLDPEVFKEMMRFIYTGRAPNLDKMADNLLAAADK
          ..K.....L...SPVF.AMFEHEMEES.KN.VEINDLDP.VFKEMMRF..T....NLDKMADNL.AAA.K
Retrocopy NLKL-TNLLVPPSPVFSAMFEHEMEESIKNRVEINDLDPDVFKEMMRFNNTRK*VNLDKMADNLWAAAGK

Parental  YAL-ERLKVMCEEALCSNLSVENVADTLVLADLHSAEQLKAQA-IDFINRCSVLRQLGCK
          .AL.E.LKVMCEE.LCSN.SVENVADTLVLADLH.AEQL.AQA.ID.IN.C.VL.QLGCK
Retrocopy HAL>EQLKVMCEEVLCSNTSVENVADTLVLADLHIAEQLEAQA<IDIINSCIVL*QLGCK

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	25.32 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	14.04 RPM
SRP007412_cerebellum	0.00 RPM	27.70 RPM
SRP007412_heart	0.00 RPM	11.25 RPM
SRP007412_kidney	0.00 RPM	9.98 RPM
SRP007412_liver	0.04 RPM	3.60 RPM
SRP007412_testis	0.00 RPM	5.35 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1884 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1884 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1884 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000014763	1 retrocopy	retro_dnov_546,
Homo sapiens	ENSG00000144228	2 retrocopies	retro_hsap_2943, retro_hsap_3048,
Gorilla gorilla	ENSGGOG00000016285	1 retrocopy	retro_ggor_2040,
Macaca mulatta	ENSMMUG00000002560	2 retrocopies	retro_mmul_1884 , retro_mmul_1885,
Nomascus leucogenys	ENSNLEG00000013800	1 retrocopy	retro_nleu_1629,
Oryctolagus cuniculus	ENSOCUG00000006944	1 retrocopy	retro_ocun_1842,
Pongo abelii	ENSPPYG00000012825	4 retrocopies	retro_pabe_2438, retro_pabe_2439, retro_pabe_2440, retro_pabe_2599,
Pan troglodytes	ENSPTRG00000012504	2 retrocopies	retro_ptro_1991, retro_ptro_2054,