RetrogeneDB ID: retro_mmul_1265

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 16:55645303..55645813(-)
• Located in intron of: ENSMMUG00000008199

Retrocopy information

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

Parental gene information

• Parental gene symbol: SH3GL3
• Ensembl ID: ENSMMUG00000013669
• Aliases: None
• Description: None

Sequence

>retro_mmul_1265
ATGTCGGTGGTGGGGCTGAAGAACCATTTCTACAAGGCAAGCCAGCTGGTCAGTGAGAAGGTGGGAGGGGCTGAGGGGAC
CAAGCTGGATGATGACTTCAAAGAGATGGAGAAGAAGGTGGATGTCACCAGCAAGGCAGTGACGGAAGTGCTGGCCAGGA
CCATCAAGTACCTGTAGCCCAACCCAAACCTCGCAGGTAAGCTGACCATGCTCAACATGGTGTCCGAGATCCGGGGCCAG
GTGAAGAACCCCAGCTATCTGCAGTTGGAGGGGCTCCTGAGCGAGTGCCTGATCTGCCACCTGAAGGAGCTGGGCGGTGA
GTCCAACTTCGGTGACACACTGCTGGATGTCGGCGAGTCCATGAAGCACCTGGTGGAGGTGAAGGACTCCCTGGACATAG
AGGTCAAACAGAACTTCATTGACCCCCTCCAGAACCTGTGCGAGAACAACCTGAAGGAGATCCAGCACCACCAGTTGGAG
GGCCGCCGCCTGGACTTTAACTAAAAGAAG

Alignment

ORF - retro_mmul_1265 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.37 %
• Parental protein coverage: 59.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVAGLKKQFHKASQLFSEKISGAEGTKLDDEFLDMERKIDVTNKAVAEILSKTTEYLQPNPAYRAKLGM
          MSV.GLK..F.KASQL.SEK..GAEGTKLDD.F..ME.K.DVT.KAV.E.L..T..YL.PNP....KL.M
Retrocopy MSVVGLKNHFYKASQLVSEKVGGAEGTKLDDDFKEMEKKVDVTSKAVTEVLARTIKYL*PNPNLAGKLTM

Parental  LNTVSKIRGQVKATGYPQTEGLLGDCMLKYGKELGEDSTFGNALIEVGESMKLMAEVKDSLDINVKQTFI
          LN.VS.IRGQVK...Y.Q.EGLL..C.....KELG..S.FG..L..VGESMK...EVKDSLDI.VKQ.FI
Retrocopy LNMVSEIRGQVKNPSYLQLEGLLSECLICHLKELGGESNFGDTLLDVGESMKHLVEVKDSLDIEVKQNFI

Parental  DPLQLLQDKDLKEIGHHLKKLEGRRLDYDYKK
          DPLQ.L....LKEI.HH...LEGRRLD...KK
Retrocopy DPLQNLCENNLKEIQHH--QLEGRRLDFN*KK

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	0.34 RPM	44.48 RPM
SRP007412_brain_prefrontal_cortex	0.32 RPM	36.89 RPM
SRP007412_cerebellum	0.45 RPM	22.41 RPM
SRP007412_heart	0.12 RPM	0.29 RPM
SRP007412_kidney	0.23 RPM	0.35 RPM
SRP007412_liver	0.55 RPM	0.04 RPM
SRP007412_testis	2.07 RPM	122.39 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1265 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1265 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1265 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003970	1 retrocopy	retro_cpor_1384,
Macaca mulatta	ENSMMUG00000000273	1 retrocopy	retro_mmul_1264,
Macaca mulatta	ENSMMUG00000013669	1 retrocopy	retro_mmul_1265 ,