RetrogeneDB ID: retro_mmul_1185

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:55315404..55316452(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.17826
• Ensembl ID: ENSMMUG00000005597
• Aliases: None
• Description: None

Sequence

>retro_mmul_1185
ATCACAGCCAAAATTGGAGGTGATGCTGCAAACAGCACTCCTGATTTTGCTTTGTGGGGCGGGGGGAGGGTAATGAGACA
GTTGGAAGATGGAGATCAACCGGAGAGCAAGAAGCTGGCTTCTCAGGGAGACGCAATCAGTTACCAACTTGGACCTATCC
ATCGTCCTCCAAGGACGTCAATGACAGAAGAGTACAAGGTCCCAGAGGGCATGGTGGGCCTGATCTTTGGCAGAGGGGGA
GAACAAATTGACAAAATCCAACAGGATTCAGCCTGCAAAGTACAGATTACTCCAGACAGCAGTGGCCTACCCGAGCACAA
TGTGTCCTTGACAGGAGCCCCAGAATCTCTACAGAAAGCGAAGATGATGCTGGATGACATTATGTCTCGGGGTCATAGAA
GGACCCCAGGACAGTTCCACAACTCCCACAGGGGCCAGAACGGTACCGTGCAGGACATGGTCCCTGTGGGGAAGGCCGGC
CTGGTCATCGCTAACGGCGGGGAGACCATGAAACAGCTGCAGGAACGCGCTGGAGTGAAGATGATCTTAATTCAGGATGG
TTCTCAGAATACCAATGTGGACAATCCTCTCCGGATCCCTGAGGATCCTTACAAAGTGCAGCAAGCCTGCGAGATGGTGA
TGGACATCCTCCAGGAACGTGACCAAGGCGGCTTTGGGGACCGGAAAGAGCAGGGATCTCGGATTGGCGGGGGCATCCAT
GTGCAGGTGCCCAGGCATTCTGTCGGCGTGATTATTGGCCGGAAAGGAGAGATGATCAAGAAGATCCAGAATGACGCTGG
TGTGAGGATACAGTTCAAGCAAGATGATGGGACAGGGCCCGAGAAGACTGCTCATATAATGGGGTCCCCAGACAGGTGCA
AGCACGCAGCCCGGATCATCAACGACCTCCTCCAGAGCCTCAGGCGTGGCCCCCCCAGGCCCTCCAGGGGGTCCAGGCAT
GCCCCCGGGGAGGCCGAGGAAGAGGCCAAGGCAACTGGGGGACCCTTGCGGGGAGATGACCTTCTCCATCCCCACTCACA
AGTGCGGG

Alignment

ORF - retro_mmul_1185 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.78 %
• Parental protein coverage: 56.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IAAKIGGDAATTVNNSTPDF---GFGGQKRQLEDGDQPESKKLASQGDSISSQLGPIHPPPRTSMTEEYR
          I.AKIGGDAA....NSTPDF...G.G...RQLEDGDQPESKKLASQGD.IS.QLGPIH.PPRTSMTEEY.
Retrocopy ITAKIGGDAA----NSTPDFALWGGGRVMRQLEDGDQPESKKLASQGDAISYQLGPIHRPPRTSMTEEYK

Parental  VPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLDDIVSRGRGGPP
          VP.GMVGLI.GRGGEQI.KIQQDS.CKVQI.PDS.GLPE..VSLTGAPES.QKAKMMLDDI.SRG....P
Retrocopy VPEGMVGLIFGRGGEQIDKIQQDSACKVQITPDSSGLPEHNVSLTGAPESLQKAKMMLDDIMSRGHRRTP

Parental  GQFHDNANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPY
          GQFH.N...GQNGTVQ..M.P.GKAGLVI..GGET.KQLQERAGVKMILIQDGSQNTNVD.PLRI..DPY
Retrocopy GQFH-NSHRGQNGTVQD-MVPVGKAGLVIANGGETMKQLQERAGVKMILIQDGSQNTNVDNPLRIPEDPY

Parental  KVQQACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQ
          KVQQACEMVMDIL.ERDQGGFGDR.E.GSRIGGGI.V.VPRHSVGV.IGR.GEMIKKIQNDAGVRIQFKQ
Retrocopy KVQQACEMVMDILQERDQGGFGDRKEQGSRIGGGIHVQVPRHSVGVIIGRKGEMIKKIQNDAGVRIQFKQ

Parental  DDGTGPEKIAHIMGPPDRCEHAARIINDLLQSLRSG-PPGPPGGPGMPP-GGRGRGRGQGNW-GPPGGEM
          DDGTGPEK.AHIMG.PDRC.HAARIINDLLQSLR.G.PPGPPGGPGMPP.GGR..GRGQGNW.G.P.GEM
Retrocopy DDGTGPEKTAHIMGSPDRCKHAARIINDLLQSLRRG>PPGPPGGPGMPP>GGR--GRGQGNW<GDPCGEM

Parental  TFSIPTHKCG
          TFSIPTHKCG
Retrocopy TFSIPTHKCG

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	0.11 RPM	41.12 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	60.21 RPM
SRP007412_cerebellum	0.00 RPM	52.50 RPM
SRP007412_heart	0.00 RPM	27.97 RPM
SRP007412_kidney	0.00 RPM	36.62 RPM
SRP007412_liver	0.00 RPM	31.51 RPM
SRP007412_testis	0.04 RPM	72.67 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1185 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1185 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1185 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4142
Pan troglodytes	retro_ptro_2814

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016627	1 retrocopy	retro_cjac_460,
Homo sapiens	ENSG00000088247	1 retrocopy	retro_hsap_4142,
Macaca mulatta	ENSMMUG00000005597	1 retrocopy	retro_mmul_1185 ,
Monodelphis domestica	ENSMODG00000001952	1 retrocopy	retro_mdom_1386,
Otolemur garnettii	ENSOGAG00000008073	1 retrocopy	retro_ogar_884,
Pan troglodytes	ENSPTRG00000010364	1 retrocopy	retro_ptro_2814,