RetrogeneDB ID: retro_mmul_2205

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:6118415..6118944(-)
• Located in intron of: ENSMMUG00000023555

Retrocopy information

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

Parental gene information

• Parental gene symbol: DUSP3
• Ensembl ID: ENSMMUG00000002351
• Aliases: None
• Description: dual specificity protein phosphatase 3 [Source:RefSeq peptide;Acc:NP_001253477]

Sequence

>retro_mmul_2205
TCCATGAAGCATCTCAATGACCCGCTCTCAGACAGCAGTGGCTGCTACAGCCTCCCAGGCCAGCCCTGCAATGAGGTCAC
CCTGAGGATTTACATGGGCAACACATCTGTGGCTCGGGAGATCCCCAAGCTTCAGAAACTGGGCATTATTCATGTCCTGA
ACACCACTGAGGGCAGGTCTTTCATGCACATAAACAATGCCAACTTCTCCAAGGACCATGGCATCACTTACCTGGGCATC
AAGGCCAAAGAAGTGCAGGAGTTCAACCTCAGCACCTACTTTGAAAGGGCTACAGACTTCACTAACCAGGCCTTGGCTCA
AAAGAATGGTCAGGTGCTCGTCCAGTGCTGGGAAGTTACAGCCATCTCCAGCTCTAGTTATGATGTACCTCATGATGTGT
CAGAAGTTGGACATCAAGTCCCTCCTGAGTATCATAAGGCAGAACTATGAGATCAGCCCCAGTGATGGGTTCCTGGCTCA
GCTTTGCCATTTCGATGACAAACTAGCCAAGGAGCGGAAGGTGAAACCC

Alignment

ORF - retro_mmul_2205 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.78 %
• Parental protein coverage: 96.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SVQDLNDLLSDGSGCYSLPSQPCNEVTPRIYVGNASVAQDIPKLQKLGITHVLNAAEGRSFMHVNTNANF
          S...LND.LSD.SGCYSLP.QPCNEVT.RIY.GN.SVA..IPKLQKLGI.HVLN..EGRSFMH.N.NANF
Retrocopy SMKHLNDPLSDSSGCYSLPGQPCNEVTLRIYMGNTSVAREIPKLQKLGIIHVLNTTEGRSFMHIN-NANF

Parental  YKDSGITYLGIKANDTQEFNLSAYFERAADFIDQALAQKNGRVLVHCRE-GYSR-SPTLVIAYLMMRQKM
          .KD.GITYLGIKA...QEFNLS.YFERA.DF..QALAQKNG.VLV.C.E..YS..SP.LV..YLMM.QK.
Retrocopy SKDHGITYLGIKAKEVQEFNLSTYFERATDFTNQALAQKNGQVLVQCWE<SYSH<SPALVMMYLMMCQKL

Parental  DVKSALSIVRQNREIGPNDGFLAQLCQLNDRLAKEGKLKP
          D.KS.LSI.RQN.EI.P.DGFLAQLC...D.LAKE.K.KP
Retrocopy DIKSLLSIIRQNYEISPSDGFLAQLCHFDDKLAKERKVKP

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	73.62 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	123.28 RPM
SRP007412_cerebellum	0.06 RPM	43.65 RPM
SRP007412_heart	0.00 RPM	77.61 RPM
SRP007412_kidney	0.00 RPM	53.99 RPM
SRP007412_liver	0.00 RPM	15.00 RPM
SRP007412_testis	0.11 RPM	26.80 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2205 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2205 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2205 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1541
Gorilla gorilla	retro_ggor_1174
Pongo abelii	retro_pabe_1277

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000108861	1 retrocopy	retro_hsap_1541,
Gorilla gorilla	ENSGGOG00000023681	1 retrocopy	retro_ggor_1174,
Macaca mulatta	ENSMMUG00000002351	1 retrocopy	retro_mmul_2205 ,
Nomascus leucogenys	ENSNLEG00000005702	1 retrocopy	retro_nleu_2391,
Pongo abelii	ENSPPYG00000008353	1 retrocopy	retro_pabe_1277,