RetrogeneDB ID: retro_mmul_2270

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:152312231..152312795(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1901
• Ensembl ID: ENSMMUG00000011467
• Aliases: None
• Description: None

Sequence

>retro_mmul_2270
AAAGGCATTCACTTTGTGATGGTCAACAGCATGGCACTGAAGGAGGACAGCTGTGGCATCTGTTCTGAAGCAGAAGCAGA
GCTTATTGAAGTTTCTTACAGACTGAATTGCTCCCGAGAGCGTTATCCTCTGTATTGGAGAAGCGACGCTAACTGTTCTG
GGGAAGATGTTGCTCCTCCGGAGGAAAAGAACATCCCATTAAAGGAGAACTATGATGTGCTTTCTTGGGAGGCATCACAA
AAGCTGCTGTGTTGGTTCCAGCTACAGCTGGATCTCAGCGGCCACATGCACAGCACCTGCGAGGTGCACCACGGGGGACA
AATCCCCGAGCTCAGCTTCCCGTCTTTCAGTTGGAGGAACAGAAACAACCCCAGTTTCACTATGGGTAGCATCACACCCA
CAGACTATGCCCTCTCCAGGTGCCACCTACCACGTGAGGACGTGGTTTTGATCATCTACTGTGGAGCGGTGGGCTTCCTT
GTGGTTCTCACACTTACTCACTTTGAGCTTTTAGCCTCACCTTTTCTTTCTGGTTTGAACCTGCTCAGAAAGCATAAGAC
AAGG

Alignment

ORF - retro_mmul_2270 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.45 %
• Parental protein coverage: 50.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KGINFVMVNSVALNGDGCGICSEAEAELIEVSHRLNCSREHYPLYRRSDANCSGDDAAPPEERDIPFKEN
          KGI.FVMVNS.AL..D.CGICSEAEAELIEVS.RLNCSRE.YPLY.RSDANCSG.D.APPEE..IP.KEN
Retrocopy KGIHFVMVNSMALKEDSCGICSEAEAELIEVSYRLNCSRERYPLYWRSDANCSGEDVAPPEEKNIPLKEN

Parental  YDVLSREASQKLLWWLQPRLVLSGHTHSACEVHHGGRVPEFSVPSFSWRNRNNPSFIMGSITPTDYALSK
          YDVLS.EASQKLL.W.Q..L.LSGH.HS.CEVHHGG..PE.S.PSFSWRNRNNPSF.MGSITPTDYALS.
Retrocopy YDVLSWEASQKLLCWFQLQLDLSGHMHSTCEVHHGGQIPELSFPSFSWRNRNNPSFTMGSITPTDYALSR

Parental  CYLPREDVVLVIYCGAVGFLVVLTLSHLGLLASPFLSGLNLLRKRKTR
          C.LPREDVVL.IYCGAVGFLVVLTL.H..LLASPFLSGLNLLRK.KTR
Retrocopy CHLPREDVVLIIYCGAVGFLVVLTLTHFELLASPFLSGLNLLRKHKTR

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	39.33 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	43.71 RPM
SRP007412_cerebellum	0.00 RPM	22.73 RPM
SRP007412_heart	0.06 RPM	10.25 RPM
SRP007412_kidney	0.00 RPM	25.82 RPM
SRP007412_liver	0.00 RPM	24.34 RPM
SRP007412_testis	0.04 RPM	48.13 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2270 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2270 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2270 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000154889	1 retrocopy	retro_hsap_1450,
Macaca mulatta	ENSMMUG00000011467	1 retrocopy	retro_mmul_2270 ,
Mus musculus	ENSMUSG00000062526	1 retrocopy	retro_mmus_869,
Otolemur garnettii	ENSOGAG00000007068	2 retrocopies	retro_ogar_1163, retro_ogar_2826,
Pongo abelii	ENSPPYG00000008997	1 retrocopy	retro_pabe_3557,
Pan troglodytes	ENSPTRG00000009872	1 retrocopy	retro_ptro_986,