RetrogeneDB ID: retro_mmul_1649

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:177026265..177026574(+)
• Located in intron of: ENSMMUG00000006770

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1746
• Ensembl ID: ENSMMUG00000021571
• Aliases: None
• Description: enhancer of rudimentary homolog [Source:RefSeq peptide;Acc:NP_001247493]

Sequence

>retro_mmul_1649
TCTCACACCATTTTGCTGGTACAGACTACCAAGAGGCCAGAAGGCAGAACTTATGCTGACTATGAATCTGTGAATGAATG
CATGGAAGGCATTTGTGAAATGTATGAAGACATGTGAAAAGAATGAATCCCAACAGTCCCTCTATCACATATGACATCAG
TCAGTTGTTTGATTTCATCAATGATCTGGCAGACCTCAGCTGCCTGGTTTACCGAGCTGATATCCAGACATACCAGCCTT
ATAAAAAAAGACTGGATTAAAGAGAAGATCTACATGCTTCTTCATCGGCAAGCTCAACAGGCTGAGAAA

Alignment

ORF - retro_mmul_1649 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.62 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SHTILLVQPTKRPEGRTYADYESVNECMEGVCKMYEE-HLKRMNPNSPSITYDISQLFDFIDDLADLSCL
          SHTILLVQ.TKRPEGRTYADYESVNECMEG.C.MYE..H.KRMNPNSPSITYDISQLFDFI.DLADLSCL
Retrocopy SHTILLVQTTKRPEGRTYADYESVNECMEGICEMYED<HVKRMNPNSPSITYDISQLFDFINDLADLSCL

Parental  VYRADTQTYQPY-NKDWIKEKIYVLLRRQAQQAGK
          VYRAD.QTYQPY..KDWIKEKIY.LL.RQAQQA.K
Retrocopy VYRADIQTYQPY>KKDWIKEKIYMLLHRQAQQAEK

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	0.78 RPM	33.95 RPM
SRP007412_brain_prefrontal_cortex	0.48 RPM	25.23 RPM
SRP007412_cerebellum	0.71 RPM	28.86 RPM
SRP007412_heart	0.00 RPM	20.26 RPM
SRP007412_kidney	0.00 RPM	24.30 RPM
SRP007412_liver	0.08 RPM	18.49 RPM
SRP007412_testis	0.11 RPM	64.19 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1649 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1649 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1649 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014529	1 retrocopy	retro_amel_1906,
Callithrix jacchus	ENSCJAG00000014940	2 retrocopies	retro_cjac_209, retro_cjac_846,
Dipodomys ordii	ENSDORG00000006912	3 retrocopies	retro_dord_250, retro_dord_406, retro_dord_562,
Equus caballus	ENSECAG00000019178	1 retrocopy	retro_ecab_45,
Macropus eugenii	ENSMEUG00000014602	3 retrocopies	retro_meug_1469, retro_meug_498, retro_meug_64,
Myotis lucifugus	ENSMLUG00000011879	1 retrocopy	retro_mluc_142,
Macaca mulatta	ENSMMUG00000021571	1 retrocopy	retro_mmul_1649 ,
Oryctolagus cuniculus	ENSOCUG00000004636	1 retrocopy	retro_ocun_42,
Otolemur garnettii	ENSOGAG00000029388	5 retrocopies	retro_ogar_1170, retro_ogar_1537, retro_ogar_2710, retro_ogar_625, retro_ogar_854,
Rattus norvegicus	ENSRNOG00000004883	3 retrocopies	retro_rnor_1721, retro_rnor_2670, retro_rnor_308,