RetrogeneDB ID: retro_mmul_1434

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:59610327..59610624(+)
• Located in intron of: ENSMMUG00000008549

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRB3
• Ensembl ID: ENSMMUG00000005599
• Aliases: None
• Description: crumbs protein homolog 3 precursor [Source:RefSeq peptide;Acc:NP_001253010]

Sequence

>retro_mmul_1434
TGGGCGCAAATACCGACCCCTTCTGCAAATGAGAGTAGCATTGTTTTGCCTACACCCACCAGCTCCGGCTCCAACGGAGC
CCTGTCTCAGGGGGGCCGTCACTGCTATCATCGTGTTCTTCTGATTCCTGGCCGTCTTGTTCCTGGCTGTGGGGCTGGCA
CTATTGGTGCGGAAGCTTCGGGAGATGCGGCAGACGGAGGGCACCTACTGGCCCAGCAGCGAGGAACAGTTCTCTTATGT
AGCTGGGCCTGGGCCCCTCAGGACTCCAATGAGACCCTGTGGGGCTACCTGCACATC

Alignment

ORF - retro_mmul_1434 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.33 %
• Parental protein coverage: 80.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WGQRLASSAYDSSTVVPSPTSSSSNGNLSQE-AITAIIVVFSILAILLLAVGLALLVWKLREKRQTEGTY
          W.Q....SA..SS.V.P.PTSS.SNG.LSQ..A.TAIIV.F..LA.L.LAVGLALLV.KLRE.RQTEGTY
Retrocopy WAQIPTPSANESSIVLPTPTSSGSNGALSQG>AVTAIIVFF*FLAVLFLAVGLALLVRKLREMRQTEGTY

Parental  RPSSEEQFSHAAE-ARAPQDSKETVRGCLPI
          .PSSEEQFS..A..A.APQDS.ET..G.L.I
Retrocopy WPSSEEQFSYVAG<AWAPQDSNETLWGYLHI

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	0.34 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	1.59 RPM
SRP007412_cerebellum	0.00 RPM	1.23 RPM
SRP007412_heart	0.00 RPM	0.18 RPM
SRP007412_kidney	0.00 RPM	8.22 RPM
SRP007412_liver	0.00 RPM	9.90 RPM
SRP007412_testis	0.00 RPM	0.11 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1434 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1434 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1434 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2747
Gorilla gorilla	retro_ggor_1910
Pongo abelii	retro_pabe_2222

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016567	1 retrocopy	retro_cjac_868,
Homo sapiens	ENSG00000130545	2 retrocopies	retro_hsap_2747, retro_hsap_3478,
Gorilla gorilla	ENSGGOG00000007070	2 retrocopies	retro_ggor_1910, retro_ggor_2345,
Macaca mulatta	ENSMMUG00000005599	1 retrocopy	retro_mmul_1434 ,
Nomascus leucogenys	ENSNLEG00000015936	1 retrocopy	retro_nleu_1543,
Pongo abelii	ENSPPYG00000009457	2 retrocopies	retro_pabe_2222, retro_pabe_2873,
Pan troglodytes	ENSPTRG00000010367	1 retrocopy	retro_ptro_2984,
Rattus norvegicus	ENSRNOG00000047322	1 retrocopy	retro_rnor_1506,
Ictidomys tridecemlineatus	ENSSTOG00000002396	1 retrocopy	retro_itri_781,