RetrogeneDB ID: retro_mmul_1103

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:70311215..70312453(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DOK1
• Ensembl ID: ENSMMUG00000002139
• Aliases: None
• Description: None

Sequence

>retro_mmul_1103
GAAGCGGGGAAGGAACCGCTGGGGGCCATGGATGGAGCTGTGATGGAAGGGCCACTCTTTTTGCAGAGTGAGCACTTTGG
GACCAAGAGGTGGAGGAAGACCTGGGCTGTGCTCTACCTGGTCAGTCCCCGTGGCATAGCGTGGCTCAGGTTCTTTGACC
ATAAGGGGTCGAGCTCTGGGAGCGGCTGAGGGAGCTCGTGCTGCCTGTACTGCAAGGTGATCCATCTGGTGAAGTGTGTG
AGTTTGGCCCCCGTGGCTGTGGAGAGCCCCCCTGAGCCCAGCGCCACTGCCTTCCGCCTGGACACTGCACAGCACTAGCA
CCTGCTGGCTGTTGATGTGCTGTCCAGTGCAGCCTGGATGCAGACACTGCCAAAACCCCTTTCGGAAAGGCAGCTGGATT
CTGGAACCTACCAACAACCCACCTGAGCTTTCTGCCCTGGAGATGCTGGAGAACTCCTTGTGCAGCCACACCTGGGAAGG
ATCCCAATTCTGGGTAACGGTGCAGAGGACTGAGGCGGCTGAGCACTGTGGCCTGCATGCCTCTATTTGCTGACGGTTGG
AGGCTGAGAGGGTGACTCTCCTGACCATGGGGGCCCAGAGTCAGATACTGGAGCTGTCCTGTCCTGGCCCTACACTCTGT
TGCATTGCTATGGCCGGGACAAGGTCGTGTTCTCTTTTGAGGCCAGCGCCACTGCCTCCTGGGCCCTGGAACCTTCACCT
TCCAGACAGCACAGGGAAATGACATCTTCCAGGCAGGTGAGACTGCCATCCACTGGCAGAAGACCCAGGGAAAGGCCAGA
CAGGGTCAGAATGTTCTCAGAGCTGACTCCCAAGAAGGAGAGGTGGCAAAGGGGAAATTCCCTTCCCTACCTGGCCCCCA
AGGGCTTCTTGACAGCCCCCCAGCCCTGTATGCTGAGCCCTTAGACTCCCTGTGCATCGCTTCAGGCCCATCCCAGCACT
CCCTATACTCAGACTTCTTGGACAGCACCCTTGCTCGGGCAGCAGAGGGAGTACAATGGAAGAAACCTCTCTATTGGGAC
TTGTACGGACATGAGCAGCAGCAGTTGCTGAAGGCCAAGCTGATGGACTCCAAACAGGATCCCATCTATGTTGAACCTGA
GGGCCTGGTCCCAGCCCTTCCCCAGAGCCTTTATGATCTGCCTTAGGAGCCCAAGGATGTGTGGGGATGCCAAGCTCAGG
TGAAGTAGGAGAGCTATGAGCTCCCCTACAACCCTGCC

Alignment

ORF - retro_mmul_1103 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.56 %
• Parental protein coverage: 74.86 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EARKEPPGAMDGAVMEGPLFLQSQRFGTKRWRKTWAVLYPASPHGVARLEFFDHKGSSSGGGRGSSRRLD
          EA.KEP.GAMDGAVMEGPLFLQS..FGTKRWRKTWAVLY..SP.G.A.L.FFDHKGSSSG.G.GSS..L.
Retrocopy EAGKEPLGAMDGAVMEGPLFLQSEHFGTKRWRKTWAVLYLVSPRGIAWLRFFDHKGSSSGSG*GSSCCLY

Parental  CKVIRLAECVSVAPVTVDTPPEPGATAFRLDTAQRSHLLAADAPSSAAWVQTL-CRNAFPK-GSWTLAPS
          CKVI.L..CVS.APV.V..PPEP.ATAFRLDTAQ..HLLA.D..SSAAW.QTL.....F.K.GSW.L.P.
Retrocopy CKVIHLVKCVSLAPVAVESPPEPSATAFRLDTAQH*HLLAVDVLSSAAWMQTL<AKTPFGK<GSWILEPT

Parental  DNPPKLSALEMLENSLYSPTWEGSQFWVTVQRTEAAERCGLHGSYVLRVETERLTLLTMGAQSQILE-PL
          .NPP.LSALEMLENSL.S.TWEGSQFWVTVQRTEAAE.CGLH.S...R.E.ER.TLLTMGAQSQILE...
Retrocopy NNPPELSALEMLENSLCSHTWEGSQFWVTVQRTEAAEHCGLHASIC*RLEAERVTLLTMGAQSQILE<AV

Parental  LSWPYTLLRRYGRDKVMFSFEAG-RRCPSGPGTFTFQTAQGNDIFQAVETAIHRQKAQGKAGQGHDVLRA
          LSWPYTLL..YGRDKV.FSFEA..R.C..GPGTFTFQTAQGNDIFQA.ETAIH.QK.QGKA.QG..VLRA
Retrocopy LSWPYTLLHCYGRDKVVFSFEAS<RHCLLGPGTFTFQTAQGNDIFQAGETAIHWQKTQGKARQGQNVLRA

Parental  DSHEGEVAEGKLPSPPGPQELLDSPPALYAEPLDSLRIAPCPSQDSLYSDPLDSTPARAGEGVQRKKPLY
          DS.EGEVA.GK.PS.PGPQ.LLDSPPALYAEPLDSL.IA..PSQ.SLYSD.LDST.ARA.EGVQ.KKPLY
Retrocopy DSQEGEVAKGKFPSLPGPQGLLDSPPALYAEPLDSLCIASGPSQHSLYSDFLDSTLARAAEGVQWKKPLY

Parental  WDLFEHAQQQLLKAKLTDPKEDPIYDEPEGLAPVPPQGLYDLPREPKDAWWCQARVKEEGYELPYNPA
          WDL..H.QQQLLKAKL.D.K.DPIY.EPEGL.P..PQ.LYDLP.EPKD.W.CQA.VK.E.YELPYNPA
Retrocopy WDLYGHEQQQLLKAKLMDSKQDPIYVEPEGLVPALPQSLYDLP*EPKDVWGCQAQVK*ESYELPYNPA

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	4.03 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	5.32 RPM
SRP007412_cerebellum	0.00 RPM	2.45 RPM
SRP007412_heart	0.00 RPM	6.89 RPM
SRP007412_kidney	0.00 RPM	4.58 RPM
SRP007412_liver	0.00 RPM	7.64 RPM
SRP007412_testis	0.00 RPM	2.60 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1103 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1103 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1103 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_891
Pan troglodytes	retro_ptro_615

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000115325	1 retrocopy	retro_hsap_891,
Macaca mulatta	ENSMMUG00000002139	1 retrocopy	retro_mmul_1103 ,
Nomascus leucogenys	ENSNLEG00000001010	1 retrocopy	retro_nleu_391,
Pongo abelii	ENSPPYG00000012264	1 retrocopy	retro_pabe_767,
Pan troglodytes	ENSPTRG00000012100	1 retrocopy	retro_ptro_615,