RetrogeneDB ID: retro_mmul_1200

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:86855002..86855661(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2165
• Ensembl ID: ENSMMUG00000021864
• Aliases: None
• Description: synaptogyrin-2 [Source:RefSeq peptide;Acc:NP_001253128]

Sequence

>retro_mmul_1200
ATGGAGAGCGGGGCCTACTATGTGGCCAACGCGGGTGGCTCCTTCCACCTGCGGCGCTTCCTGACGCAACCGCAGGTGGC
GGCGCGCGCCCTGTGCAGGATCTTTGCCTTGATCGTGTTCTCCTGCATCTATGGCGAGGACTACAGCAAGTCTAAGCAGA
TGTACTGCGTGTTCAACCACAACGAGGACGCCTGCCGCTACGGCAGTGTCATTGGGGTGCTGGCCTTCGAGGCCTCGGCC
TTCTTGGTGGCCGACGCGTATTTCCCCCAGATCAGCAACGCCACTGACCGCAAGTACCTGGTCATTGGTGACCTGCTCTT
CTCAGCTCTCTGAACCTTCCTGTGGTTTGTTGATTTCGGCTTCCTTACTAACCAGTGGGTGGCCACCCAACCGGAGGACG
TGCCGCTGGGGGCCAACTCCACGCGGACAGCCATCACTTTCAGCTTCTTTTCCATCTTCTCCTGGGGCGTGCTGGCCTTC
CTGGCCTATCGGCGCTGCAAGGCTGGCGTGGAGGACTTCATCCAGAACTACATCGACTCCACCCCAGACCTCAACACTGC
CTACGCCTCCTACCCAGGTGCATCTGTGGACAACTACCAGCAGCTGCCCTTCACCCAGAATACGGAGACCACCGAGGGCT
ACCAGCCGCCCCTGTGTAC

Alignment

ORF - retro_mmul_1200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.56 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MESGAYGAAKAGGSFDLRRFLTQPQVVARAVCLVFALIVFSCIYGEGYSNTHKSKQMYCVFNHNEDACRY
          MESGAY..A.AGGSF.LRRFLTQPQV.ARA.C..FALIVFSCIYGE.YS...KSKQMYCVFNHNEDACRY
Retrocopy MESGAYYVANAGGSFHLRRFLTQPQVAARALCRIFALIVFSCIYGEDYS---KSKQMYCVFNHNEDACRY

Parental  GSAIGVLAFLASAFFLVIDAYFPQISNATDRKYLVIGDLLFSALWTFLWFVGFCFLTNQWAATDPKDVLV
          GS.IGVLAF.ASAF.LV.DAYFPQISNATDRKYLVIGDLLFSAL.TFLWFV.F.FLTNQW.AT.P.DV..
Retrocopy GSVIGVLAFEASAF-LVADAYFPQISNATDRKYLVIGDLLFSAL*TFLWFVDFGFLTNQWVATQPEDVPL

Parental  GADSARAAITFSFFSIFSWGVLASLAYQRYKAGVDDFIQNYVDPTPDPNTAYASYPGASVDNYQQPPFTQ
          GA.S.R.AITFSFFSIFSWGVLA.LAY.R.KAGV.DFIQNY.D.TPD.NTAYASYPGASVDNYQQ.PFTQ
Retrocopy GANSTRTAITFSFFSIFSWGVLAFLAYRRCKAGVEDFIQNYIDSTPDLNTAYASYPGASVDNYQQLPFTQ

Parental  NAETTEGYQPP-PVY
          N.ETTEGYQPP.PVY
Retrocopy NTETTEGYQPP<PVY

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	5.38 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	9.84 RPM
SRP007412_cerebellum	0.00 RPM	4.26 RPM
SRP007412_heart	0.00 RPM	42.87 RPM
SRP007412_kidney	0.00 RPM	27.35 RPM
SRP007412_liver	0.00 RPM	53.40 RPM
SRP007412_testis	0.04 RPM	23.82 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1200 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1200 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1200 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3487

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000108639	2 retrocopies	retro_hsap_1472, retro_hsap_4275,
Macaca mulatta	ENSMMUG00000021864	1 retrocopy	retro_mmul_1200 ,
Pongo abelii	ENSPPYG00000008684	2 retrocopies	retro_pabe_1220, retro_pabe_3487,
Ictidomys tridecemlineatus	ENSSTOG00000006834	1 retrocopy	retro_itri_705,