RetrogeneDB ID: retro_mmul_414

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:130935775..130936055(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000009039
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HMGN3
• Ensembl ID: ENSMMUG00000004351
• Aliases: None
• Description: None

Sequence

>retro_mmul_414
TCTTCAGAGAATACAGAGGGCGAAGATGGCTCCAAAGTAACTAAACAGGAGCCCACAAGATGGTCTCCCAGATGGTCAGT
AAAACCTCCTCCACCAAAACCTGCACCCAAACAAAGAAAAACATCTGCTGAGAAAGAACCTGGAGCAAAGGTTAGCAGAG
GTGCTAAAGGGAAGAAAGGAAAAGCAGGAAGCTGGAAAGGAAGGTACTGCACCATCTGAAAATGATAAAACTAAAGCTGA
AGAGGCACAGAAAACTGAATCTGTAGTTAACCAGGGAGAA

Alignment

ORF - retro_mmul_414 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.95 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SPENTEGKDGSKVTKQEPTRRSARLSAKPAPPKPEPKPRKTSAKKEPGAKISRGAKGK-KEEKQEAGKEG
          S.ENTEG.DGSKVTKQEPTR.S.R.S.KP.PPKP.PK.RKTSA.KEPGAK.SRGAKGK.KE....AGKEG
Retrocopy SSENTEGEDGSKVTKQEPTRWSPRWSVKPPPPKPAPKQRKTSAEKEPGAKVSRGAKGK>KEKQE-AGKEG

Parental  TAPSENGETKAEEAQKTESVDNEGE
          TAPSEN..TKAEEAQKTESV.N.GE
Retrocopy TAPSENDKTKAEEAQKTESVVNQGE

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	25.44 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	12.61 RPM
SRP007412_cerebellum	0.00 RPM	29.70 RPM
SRP007412_heart	0.00 RPM	67.84 RPM
SRP007412_kidney	0.00 RPM	36.50 RPM
SRP007412_liver	0.00 RPM	7.52 RPM
SRP007412_testis	0.00 RPM	6.71 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_414 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_414 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_414 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_231
Pan troglodytes	retro_ptro_200
Pongo abelii	retro_pabe_421

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007015	1 retrocopy	retro_chof_2241,
Cavia porcellus	ENSCPOG00000012407	2 retrocopies	retro_cpor_1399, retro_cpor_147,
Felis catus	ENSFCAG00000028793	1 retrocopy	retro_fcat_1400,
Homo sapiens	ENSG00000118418	1 retrocopy	retro_hsap_231,
Gorilla gorilla	ENSGGOG00000006910	1 retrocopy	retro_ggor_293,
Macaca mulatta	ENSMMUG00000004351	1 retrocopy	retro_mmul_414 ,
Nomascus leucogenys	ENSNLEG00000012377	2 retrocopies	retro_nleu_68, retro_nleu_851,
Otolemur garnettii	ENSOGAG00000016487	1 retrocopy	retro_ogar_190,
Ochotona princeps	ENSOPRG00000009611	1 retrocopy	retro_opri_799,
Pan troglodytes	ENSPTRG00000018366	2 retrocopies	retro_ptro_1427, retro_ptro_200,
Ictidomys tridecemlineatus	ENSSTOG00000014353	1 retrocopy	retro_itri_251,
Tupaia belangeri	ENSTBEG00000015468	3 retrocopies	retro_tbel_1912, retro_tbel_4714, retro_tbel_615,
Tarsius syrichta	ENSTSYG00000005238	3 retrocopies	retro_tsyr_1569, retro_tsyr_268, retro_tsyr_976,