RetrogeneDB ID: retro_mmul_1936

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:23648738..23649622(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.716
• Ensembl ID: ENSMMUG00000009499
• Aliases: None
• Description: mesoderm specific transcript homolog [Source:RefSeq peptide;Acc:NP_001247871]

Sequence

>retro_mmul_1936
AGGATGAGGTAGTGGCCGGTCCGGTTGGGGCTGTTGGCCCTGACCCTCCTTGCTGTGTACCTGCACATCCCACCTCTTCA
GGTGTCCCCTGCCCTTCACTCATAGAAGTCTTTAGGAAAGTTGTTCACTTACAAAGGACTGTGTATCTTCTACCAAGATT
TTGTGGGTGTGCTTGGAAGTCCGGAGATAGTTGGGCGTTTACACGGCTTTCCAACATCCAGCTACAATTGGTACAACTTT
GGGAAGTTTGACCTTGAGGTCTTATCGAGTGATTGTCCTTGATTTCTCAGGCTTTGGCTTCAGTGACAAACGGAGACCAC
ATCACTATTCCATATTTGAGCAGGCCAGCATTGTGGAAGCGCTTTGGGGCATCTGGAGCTCCAGAACGGCAGGATCAACC
TTTAGTCTCATGACTATGGAGATATTGTTGCTCAGGAACTGCTCTACAGGCACAAGCATAATCTGTCTGGTCGGCTTACC
ATAAAGAGTCTCTGTCTGTCAAATGGAGGTATCTTTCCTGAGACTCGCCGTACACTCCTCCAAAAGCTACTCACAGGTGG
AGGTGTGCTGCCACCCATCCTCACGCAGCTGGTGAACTTTGTATTCTCTTGAGGTCTCACCCCAGTCTTTGGGCCGTATA
CTCGGCCCTCTGAGAGTGAGCTGTGGGACATGTGGGCAGGGATCCTCAACAATGACAGAAACTTAGTCATTGTTAGTCTC
TTCCATCAATAGAGGAACTAGTTCAGAAGGCGCTGTGTGGGAGTTCTTGCCTCTGTAACTATCCCTATTCATTTTATCTG
TGGGCCTTGGATCCTGTGAACCCCTACCCAGAGTTTTTGGAGCTGTACAGGAAAATGCTGCCGTGGTCTACATTAGCCGC
GATC

Alignment

ORF - retro_mmul_1936 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.63 %
• Parental protein coverage: 89.55 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RMREWWVQVGLLAVPLLAAYLHIPPPQLSPALHSWKSSGKFFTYKGLRIFYQDSVGVVGSPEIVVLLHGF
          RMR.W.V..GLLA..LLA.YLHIPP.Q.SPALHS.KS.GK.FTYKGL.IFYQD.VGV.GSPEIV..LHGF
Retrocopy RMR*WPVRLGLLALTLLAVYLHIPPLQVSPALHS*KSLGKLFTYKGLCIFYQDFVGVLGSPEIVGRLHGF

Parental  PTSSYDWY-KIWE-GLTLRFHRVIALDFLGFGFSDKPRPHHYSIFEQASIVEAL-LRHLGLQNRRINLLS
          PTSSY.WY...WE..LTLR..RVI.LDF.GFGFSDK.RPHHYSIFEQASIVEAL.L.HL.LQN.RINL.S
Retrocopy PTSSYNWY<QLWE<SLTLRSYRVIVLDFSGFGFSDKRRPHHYSIFEQASIVEAL<LGHLELQNGRINL*S

Parental  HDYGDTVAQELLYRYKQNRSGRLTIKSLCLSNGGIFPETHRPLLLQKLLKDGGVLSPILTRLMNFFVFSR
          HDYGD.VAQELLYR.K.N.SGRLTIKSLCLSNGGIFPET.R..LLQKLL..GGVL.PILT.L.N.FVFS.
Retrocopy HDYGDIVAQELLYRHKHNLSGRLTIKSLCLSNGGIFPETRR-TLLQKLLTGGGVLPPILTQLVN-FVFS*

Parental  GLTPVFGPYTRPSESELWDMWAGIRNNDGNLVIDSLLQYINQRKKFRRRWVGALASVTIPIHFIYGP-LD
          GLTPVFGPYTRPSESELWDMWAGI.NND.NLVI.SL......R..FRRR.VG.LASVTIPIHFI.GP.LD
Retrocopy GLTPVFGPYTRPSESELWDMWAGILNNDRNLVIVSL--FHQ*RN*FRRRCVGVLASVTIPIHFICGP<LD

Parental  PVNPYPEFLELYRKTLPRSTVSIL
          PVNPYPEFLELYRK.LP.ST....
Retrocopy PVNPYPEFLELYRKMLPWSTLAAI

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	32.16 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	45.22 RPM
SRP007412_cerebellum	0.00 RPM	18.60 RPM
SRP007412_heart	0.00 RPM	8.95 RPM
SRP007412_kidney	0.00 RPM	9.51 RPM
SRP007412_liver	0.00 RPM	15.56 RPM
SRP007412_testis	0.00 RPM	17.68 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1936 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1936 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1936 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005659	2 retrocopies	retro_amel_1177, retro_amel_1874,
Callithrix jacchus	ENSCJAG00000010760	2 retrocopies	retro_cjac_1563, retro_cjac_3931,
Felis catus	ENSFCAG00000022984	5 retrocopies	retro_fcat_1067, retro_fcat_1645, retro_fcat_1693, retro_fcat_2004, retro_fcat_326,
Loxodonta africana	ENSLAFG00000006066	3 retrocopies	retro_lafr_578, retro_lafr_584, retro_lafr_748,
Macropus eugenii	ENSMEUG00000008227	1 retrocopy	retro_meug_885,
Microcebus murinus	ENSMICG00000006129	1 retrocopy	retro_mmur_1091,
Macaca mulatta	ENSMMUG00000009499	2 retrocopies	retro_mmul_1936 , retro_mmul_94,
Nomascus leucogenys	ENSNLEG00000012841	3 retrocopies	retro_nleu_1065, retro_nleu_515, retro_nleu_790,
Otolemur garnettii	ENSOGAG00000009224	1 retrocopy	retro_ogar_3464,
Pongo abelii	ENSPPYG00000018006	4 retrocopies	retro_pabe_2337, retro_pabe_2510, retro_pabe_2511, retro_pabe_866,
Pan troglodytes	ENSPTRG00000019698	2 retrocopies	retro_ptro_1769, retro_ptro_2045,
Sorex araneus	ENSSARG00000000502	1 retrocopy	retro_sara_352,
Ictidomys tridecemlineatus	ENSSTOG00000020977	2 retrocopies	retro_itri_1210, retro_itri_1610,
Tupaia belangeri	ENSTBEG00000008404	2 retrocopies	retro_tbel_1480, retro_tbel_526,
Tursiops truncatus	ENSTTRG00000004934	4 retrocopies	retro_ttru_1026, retro_ttru_1115, retro_ttru_1133, retro_ttru_1907,