RetrogeneDB ID: retro_mmul_1464

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:133012172..133012743(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.3197
• Ensembl ID: ENSMMUG00000019593
• Aliases: None
• Description: synaptophysin-like protein 1 [Source:RefSeq peptide;Acc:NP_001253746]

Sequence

>retro_mmul_1464
CTCAAAGAGCTGCTTGACGTCAATATTCTCCAATAGATCGTTTCCATCTGTGCTTTTACCACTTGTGGAGATTTTACGGA
CAAAACTGCTATTTGAATAAGTTGTTCTCCTAAAATTGCTGGCATTAAAACAACTACAGCTATTTTTTGGTTATCCATGC
AGGTTGAATCAGGCATCATTTTAGTCACCTCCAGATGTAAATGTGTGAGATGTAAATTGGCAAAATCATGTCTTTACAGG
AGATTTCTCTTCTTCTGCACAATTCTGTCTTATATTTGCAGTCTTTGTCTTCTTGTATTGCATTTCTGCTCTTCTGCTTT
ATGTTGGTTACATGAACACATATGGGCACAGTCAAAAAACTTTTCATAACTGACTTTGTTGCTCCTCTTTTTGCCACTTT
TTGAGGTTAGTGAGCCTTTCAACCTAGGCTAAAGCTCTTACAAATACTAAAATAGCTACCAGTCACAATAATGTTCAGGA
ACTTCTGCCTTGCAAACAGCCAAGAGTCACATGTTTCTTTGGCTCTATGACTAGCGTGGGGTCCCTAAATGGATCCGTGA
TATTTGGTTTT

Alignment

ORF - retro_mmul_1464 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.34 %
• Parental protein coverage: 79.25 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LKEPLGFIKVLEWIASIFAFATCGGFKGQTEIQVSCPPTITENKTITATF-GYPFRLNEASFQPPPGVNI
          LKE.L.....L..I.SI.AF.TCG.F...T.I..SC.P.I...KT.TA.F.GYP.RLN.ASF..PP.VN.
Retrocopy LKELLD-VNILQ*IVSICAFTTCGDFTDKTAI*ISCSPKIAGIKTTTAIF>GYPCRLNQASF*SPPDVNV

Parental  CDVNWKSYVLIGDYSSSAQFYVTFAVFVFLYCIAALLLYVGYTSLYLDS-RKLPMIDFVVTLVAT-FLWL
          .DVNW...V..GD.SSSAQF...FAVFVFLYCI.ALLLYVGY...Y..S..KL...DFV..L.AT.FL.L
Retrocopy *DVNWQNHVFTGDFSSSAQFCLIFAVFVFLYCISALLLYVGYMNTYGHS>KKLFITDFVAPLFAT<FLRL

Parental  VSTSAWAKALTDIKIATGHNIVQELSPCKKKEILCYFGSVTSMGSLNVSVIFGF
          VS.S..AKALT..KIAT.HN.VQEL.PCK.....C.FGS.TS.GSLN.SVIFGF
Retrocopy VSLST*AKALTNTKIATSHNNVQELLPCKQPRVTCFFGSMTSVGSLNGSVIFGF

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	18.38 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	9.44 RPM
SRP007412_cerebellum	0.00 RPM	15.95 RPM
SRP007412_heart	0.00 RPM	31.44 RPM
SRP007412_kidney	0.00 RPM	131.10 RPM
SRP007412_liver	0.00 RPM	22.25 RPM
SRP007412_testis	0.00 RPM	79.27 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1464 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1464 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1464 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1939
Callithrix jacchus	retro_cjac_1588

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016176	2 retrocopies	retro_cjac_1588, retro_cjac_2483,
Cavia porcellus	ENSCPOG00000009221	1 retrocopy	retro_cpor_239,
Equus caballus	ENSECAG00000009695	1 retrocopy	retro_ecab_340,
Homo sapiens	ENSG00000008282	1 retrocopy	retro_hsap_1817,
Gorilla gorilla	ENSGGOG00000006497	1 retrocopy	retro_ggor_1984,
Myotis lucifugus	ENSMLUG00000014980	3 retrocopies	retro_mluc_1884, retro_mluc_2083, retro_mluc_449,
Macaca mulatta	ENSMMUG00000019593	2 retrocopies	retro_mmul_1251, retro_mmul_1464 ,
Mus musculus	ENSMUSG00000020570	1 retrocopy	retro_mmus_3470,
Nomascus leucogenys	ENSNLEG00000008861	1 retrocopy	retro_nleu_2720,
Oryctolagus cuniculus	ENSOCUG00000015127	3 retrocopies	retro_ocun_1000, retro_ocun_1569, retro_ocun_331,
Otolemur garnettii	ENSOGAG00000008079	2 retrocopies	retro_ogar_1970, retro_ogar_2520,
Ochotona princeps	ENSOPRG00000006755	2 retrocopies	retro_opri_210, retro_opri_448,
Pongo abelii	ENSPPYG00000018292	1 retrocopy	retro_pabe_2370,
Pan troglodytes	ENSPTRG00000019570	2 retrocopies	retro_ptro_1173, retro_ptro_1939,
Rattus norvegicus	ENSRNOG00000009856	2 retrocopies	retro_rnor_2273, retro_rnor_2992,
Sorex araneus	ENSSARG00000013935	1 retrocopy	retro_sara_450,
Ictidomys tridecemlineatus	ENSSTOG00000020871	1 retrocopy	retro_itri_1243,
Tupaia belangeri	ENSTBEG00000009095	2 retrocopies	retro_tbel_2025, retro_tbel_2566,
Tarsius syrichta	ENSTSYG00000013296	2 retrocopies	retro_tsyr_1768, retro_tsyr_775,
Tursiops truncatus	ENSTTRG00000002848	1 retrocopy	retro_ttru_661,