RetrogeneDB ID: retro_mmul_2308

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:111834986..111835352(+)
• Located in intron of: ENSMMUG00000000975

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYNJ2BP
• Ensembl ID: ENSMMUG00000011086
• Aliases: None
• Description: synaptojanin-2-binding protein [Source:RefSeq peptide;Acc:NP_001247889]

Sequence

>retro_mmul_2308
TCAGGGCTGGGCTTCAACATCGTAGGTGGGACAGATCAGCAGTATGTCTCCAACGACAGTGGCATCTACGTCAGCCACAT
CAAAGAAAATGGGGCTGCGGCCCTGGATGGGCGGCTCCAGGAGCGTGATAAGATCCTTTCAATAAATGGCCAAGACCTAA
AGAACCTGCTGCACCAGAATGCTGTAGACCTCTTTCGTAATGCAGGTTATGCTGTGTCTCTGAGAGTGCAGCATAGGTTA
CAGGTACAGAATGGACCTATAGGTGAAGGGGACCCAAGTGGTATTCCCATATTTATGGTGCTGGTGCCAGTGTTTGCCCT
CACCATGGTAGCAGCCTGGGTTTTCATGAGATACCGGCAACAACTT

Alignment

ORF - retro_mmul_2308 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.4 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGLGFNIVGGTDQQYVSNDSGIYVSRIKENGAAALDGRLQEGDKILSVNGQDLKNLLHQDAVDLFRNAGY
          SGLGFNIVGGTDQQYVSNDSGIYVS.IKENGAAALDGRLQE.DKILS.NGQDLKNLLHQ.AVDLFRNAGY
Retrocopy SGLGFNIVGGTDQQYVSNDSGIYVSHIKENGAAALDGRLQERDKILSINGQDLKNLLHQNAVDLFRNAGY

Parental  AVSLRVQHRLQVQNGPIGHRGEGDPSGIPIFMVLVPVFALTMVAAWVFMRYRQQL
          AVSLRVQHRLQVQNGPIG...EGDPSGIPIFMVLVPVFALTMVAAWVFMRYRQQL
Retrocopy AVSLRVQHRLQVQNGPIG---EGDPSGIPIFMVLVPVFALTMVAAWVFMRYRQQL

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	0.45 RPM	2.35 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	4.44 RPM
SRP007412_cerebellum	0.19 RPM	1.81 RPM
SRP007412_heart	0.35 RPM	4.24 RPM
SRP007412_kidney	0.35 RPM	5.63 RPM
SRP007412_liver	0.24 RPM	3.80 RPM
SRP007412_testis	0.45 RPM	13.87 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2308 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2308 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2308 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007586	1 retrocopy	retro_btau_1114,
Dipodomys ordii	ENSDORG00000010450	1 retrocopy	retro_dord_443,
Macaca mulatta	ENSMMUG00000011086	1 retrocopy	retro_mmul_2308 ,
Mus musculus	ENSMUSG00000090935	3 retrocopies	retro_mmus_1428, retro_mmus_1538, retro_mmus_1802,
Otolemur garnettii	ENSOGAG00000013211	1 retrocopy	retro_ogar_1515,