RetrogeneDB ID: retro_mmul_1885

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:60752518..60753423(+)
• 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_1885
TTAGTCAGCTTTCCAAAAAGTGAAGTGTGAGCAAAATTCAAATTTTCCCTTCTGAATGCCAAAAGGGAAGAAATAAAAGC
AATGGAAAGCCAAAGAGCATATCAATTCGTGCAAGGGAAGGACTGAGATTTTAAAAAATTCATTAGAGGGAAACTTTAGC
TTGACGAAGCTAATAGTCTTTTACCAGATGACAAGCTTACATTATTTTGCAAGATGAGTGTGGTCCAAGATTCAGTAAAC
ATATCAGAACATACTAATACAATTACTTTGAAGGTGGCTGAGTGTCGACTAGAAGATGTAGGTAATCTCTGGGAAAACAG
GAGATTTACAGACTGCAGTTTTGTTGTGAGAGGAGAAGAATGTAAAGCTTTTAAATCTGCTTGTACCTCAATCCCCAGTT
TTTAATGCCATGTTTGAACATGAAATGGAAGAAAGCATAAAGAATTGAGTGGAAATAAATTATTTAGACGCTGATATTTT
TAAAGAAATGATGAGATGTATTAACACAGGGAAAGGATTAAACCTTGACAAAATGGCTGAAAACTTGTTGGCAGCTGCAG
ACAAACATGCACTGGGAACAGCTGAAGGTCATGTGTGAGGAAGCTTTGTCTAGTAATCTCTCAATAGAAAATATTGCTGA
TACCCTTGTCCTTGCAGATTTGCACTTTGCAGAACAATTGAAAGCACAAGCCATAGACATTATTAATAGGTGCATTGTAC
TTCGACAACTTGGGTGTAAACATAAGAAAAACTGGAACAGCAACCAAGCAACCGATGTAATGGAAACATCAAGGGGGAAG
TCCATGATTCAGTCTCACCCTTACTTAGTAGCAGAAGCCTTCTGAGCACTAGCATCTGCACAGTGTCCACAGTTTGGCAT
TCCAAACAAATGGCTAAAACAGTCA

Alignment

ORF - retro_mmul_1885 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 77.3 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LVSCPKSEVRAKFKFSLLNAKREETKAMESQRAYRFVQGKDWGFKKFIRRDFLLDEANGLLPDDKLTLFC
          LVS.PKSEV.AKFKFSLLNAKREE.KAMESQRAY.FVQGKD..FKKFIR....LDEAN.LLPDDKLTLFC
Retrocopy LVSFPKSEV*AKFKFSLLNAKREEIKAMESQRAYQFVQGKD*DFKKFIRGKL*LDEANSLLPDDKLTLFC

Parental  EVSVVQDSVNISGHTNTNTLKVPECRLAEDLGNLWENTRFTDCSFFVRGQEFKAHKSVLAARSPVF-NAM
          ..SVVQDSVNIS.HTNT.TLKV.ECRL.ED.GNLWEN.RFTDCSF.VRG.E.KA.KS......P.F.NAM
Retrocopy KMSVVQDSVNISEHTNTITLKVAECRL-EDVGNLWENRRFTDCSFVVRGEECKAFKSACTS-IPSF>NAM

Parental  FEHEMEESKKNQVEINDLDPEVFKEMMRFIYTGRAPNLDKMADNLLAAADKYAL-ERLKVMCEEALCSNL
          FEHEMEES.KN.VEIN.LD...FKEMMR.I.TG...NLDKMA.NLLAAADK.AL.E.LKVMCEEAL.SNL
Retrocopy FEHEMEESIKN*VEINYLDADIFKEMMRCINTGKGLNLDKMAENLLAAADKHAL>EQLKVMCEEALSSNL

Parental  SVENVADTLVLADLHSAEQLKAQAIDFINRCSVLRQLGCKDGKNWNSNQATDIMETSGWKSMIQSHPHLV
          S.EN.ADTLVLADLH.AEQLKAQAID.INRC.VLRQLGCK..KNWNSNQATD.METS..KSMIQSHP.LV
Retrocopy SIENIADTLVLADLHFAEQLKAQAIDIINRCIVLRQLGCKHKKNWNSNQATDVMETSRGKSMIQSHPYLV

Parental  AEAFRALASAQCPQFGIPRKRLKQS
          AEAF.ALASAQCPQFGIP.K.LKQS
Retrocopy AEAF*ALASAQCPQFGIPNKWLKQS

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	0.00 RPM	3.60 RPM
SRP007412_testis	0.04 RPM	5.35 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1885 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1885 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1885 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,