RetrogeneDB ID: retro_mmul_1847

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:98419382..98420178(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1975
• Ensembl ID: ENSMMUG00000007456
• Aliases: None
• Description: None

Sequence

>retro_mmul_1847
ATTCAGGTAACCAGAGATAAGAATTATGAGCCCATTGAAATACCATCAGAAGACGATGGAACAGTGCTGCTGCCCACGGT
TGCAGTTCAGTTTCCAGGGGCATGTGGGCTCCCCTACAGGATTCCAGTGTCCCAGGGTATTAGGGGTGTCTGCTGGTAGA
AGGAATTCTGCATGCCCCCAATGCTGGCTGGGGAAATGTGATATATGTTGTCAACTATTCTGTAGATAACTACAGAAAAA
GGGATAAGACAGATATTTCATTAGCCATAAAAGTGAAAAGAGCAGTCCCGAAAACATCTGCTTTAACAGTGTGGGTTTCC
CATGGAAAACAACTGAACAGGATCTGAAAGAATATTGCAGTACCTTCAGAGAAATTCTTATGGTGTAGGTCAAGAAGGAT
CTCAGAACTGGCTATTCAAAGGGATTTGGCTTTGTTCATTTTATAAAATATGAAACCCAGGTGAAAGAATGTCACAGCAA
CATAAGACAGATAGATGATGATGTGGCTGTACGCTTCCTAATTCTAAGCAAACTCTGAATGAGATTTTGAGAAGCAAAAA
TATGTTTCTTAGGTGTTGTACAGAGAAGATGAATTCTGATAAGCTTCAGCAGTTCTTTTGTCATTGCAGAGAAGTGATAG
ATGTCTTCATTCCCAAACCACTCAGGAACTTTGCCTTTCTTACATTGCAGATGATTAGCTTGTGCAGTCTCTTTGTGGAG
AGGAGTTGATTATTAAGGGAATCAGCATACATATATCCAATGCAAGTGTAAGCACAATATCAGTAGACAGAAAGAG

Alignment

ORF - retro_mmul_1847 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.01 %
• Parental protein coverage: 64.49 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  IRVTEDENDEPIEIPSEDDGTVLLSTVTAQFPGACGLRYRNPVSQCMRGV-RLVEGILHAPDAGWGNLVY
          I.VT.D.N.EPIEIPSEDDGTVLL.TV..QFPGACGL.YR.PVSQ..RGV..LVEGILHAP.AGWGN..Y
Retrocopy IQVTRDKNYEPIEIPSEDDGTVLLPTVAVQFPGACGLPYRIPVSQGIRGV<LLVEGILHAPNAGWGNVIY

Parental  VVNYPKDNKRKMDETDASSAVKVKRAVQKTSDLIV-LGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTG
          VVNY..DN.RK.D.TD.S.A.KVKRAV.KTS.L.V..G.PWKTTEQDLKEY.STF.E.LMV.VKKDL.TG
Retrocopy VVNYSVDNYRKRDKTDISLAIKVKRAVPKTSALTV<VGFPWKTTEQDLKEYCSTFREILMV*VKKDLRTG

Parental  HSKGFGFVRFTEYETQVKV-MSQRHMIDGRWCDCKLPNSKQSQDEPLRSRKVFVGRCTEDMTEDELREFF
          .SKGFGFV.F..YETQVK..MSQ.H..D...C.C.LPNSKQ...E.LRS...F...CTE.M..D.L..FF
Retrocopy YSKGFGFVHFIKYETQVKE<MSQQHKTDR**CGCTLPNSKQTLNEILRSKNMFLRCCTEKMNSDKLQQFF

Parental  SQYGDVMDVFIPKPFRAFAFVT-FADDQIAQSLCGEDLIIKGISVHISNA-EPKHNSNRQLE
          .....V.DVFIPKP.R.FAF.T..ADD...QSLCGE.LIIKGIS.HISNA...KHN..RQ.E
Retrocopy CHCREVIDVFIPKPLRNFAFLT<IADD*LVQSLCGEELIIKGISIHISNA<KCKHNISRQKE

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	119.67 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	87.90 RPM
SRP007412_cerebellum	0.00 RPM	184.17 RPM
SRP007412_heart	0.00 RPM	102.70 RPM
SRP007412_kidney	0.00 RPM	98.71 RPM
SRP007412_liver	0.00 RPM	69.03 RPM
SRP007412_testis	0.00 RPM	106.26 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1847 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1847 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1847 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3637
Pan troglodytes	retro_ptro_2460
Callithrix jacchus	retro_cjac_2457

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002381	2 retrocopies	retro_cjac_2457, retro_cjac_525,
Dasypus novemcinctus	ENSDNOG00000008531	1 retrocopy	retro_dnov_2262,
Homo sapiens	ENSG00000120948	2 retrocopies	retro_hsap_1209, retro_hsap_3637,
Macaca mulatta	ENSMMUG00000007456	1 retrocopy	retro_mmul_1847 ,
Mus musculus	ENSMUSG00000041459	1 retrocopy	retro_mmus_1958,
Nomascus leucogenys	ENSNLEG00000009512	2 retrocopies	retro_nleu_201, retro_nleu_819,
Pongo abelii	ENSPPYG00000001894	1 retrocopy	retro_pabe_1008,
Pan troglodytes	ENSPTRG00000000136	2 retrocopies	retro_ptro_2460, retro_ptro_828,
Sus scrofa	ENSSSCG00000023126	1 retrocopy	retro_sscr_652,
Tarsius syrichta	ENSTSYG00000004077	1 retrocopy	retro_tsyr_2004,
Drosophila melanogaster	FBgn0025790	1 retrocopy	retro_dmel_17,