RetrogeneDB ID: retro_mmul_1716

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:119816794..119817110(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1759
• Ensembl ID: ENSMMUG00000014055
• Aliases: None
• Description: AP-1 complex subunit sigma-2 [Source:RefSeq peptide;Acc:NP_001181839]

Sequence

>retro_mmul_1716
AGATATCTGAAGATTGTTTACAAAAGATATGCCAGTTTGTATATTTGCTGTGCTACTGCGAATCAGGGCAATGAACTAAG
TACCCTGGAAACGATTCATCATGACATGGAATTATTTGACAAGTATTTTGGCAGTGTATGTGAACTTAATATCATCTTTA
ATTTTGAAGAGGTTTATTTTATTTTGGATGAGTTCTTTTGGGAGGGGAAGTTAGGAAACCTCCAAGAAAAATGTCCTTAA
GGCAATTCCACAGGCTTATCTACCACAGGAGGAAGCTTAAACCCCACACAGAGTTCTCAAAGAAACTGGACTGACA

Alignment

ORF - retro_mmul_1716 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.93 %
• Parental protein coverage: 67.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RDLKIVYKRYASLYFCCAIEDQDNELITLEIIHRYVELLDKYFGSVCELDIIFNFEKAYFILDEF-LLGG
          R.LKIVYKRYASLY.CCA...Q.NEL.TLE.IH...EL.DKYFGSVCEL.IIFNFE..YFILDEF.LLGG
Retrocopy RYLKIVYKRYASLYICCATANQGNELSTLETIHHDMELFDKYFGSVCELNIIFNFEEVYFILDEF<LLGG

Parental  EVQ-ETSKKNVLKAIEQADLLQEEAETPRSVLEEIGLT
          EV..ETSKKNVLKAI.QA.L.QEEA.TP..VL.E.GLT
Retrocopy EVR<ETSKKNVLKAIPQAYLPQEEA*TPHRVLKETGLT

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	51.66 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	34.19 RPM
SRP007412_cerebellum	0.00 RPM	61.41 RPM
SRP007412_heart	0.00 RPM	47.82 RPM
SRP007412_kidney	0.00 RPM	7.51 RPM
SRP007412_liver	0.00 RPM	3.33 RPM
SRP007412_testis	0.00 RPM	10.48 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1716 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1716 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1716 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004393	1 retrocopy	retro_cjac_2312,
Dasypus novemcinctus	ENSDNOG00000013888	1 retrocopy	retro_dnov_1786,
Homo sapiens	ENSG00000182287	1 retrocopy	retro_hsap_1849,
Macaca mulatta	ENSMMUG00000003123	1 retrocopy	retro_mmul_17,
Macaca mulatta	ENSMMUG00000014055	1 retrocopy	retro_mmul_1716 ,
Monodelphis domestica	ENSMODG00000017197	7 retrocopies	retro_mdom_1189, retro_mdom_1329, retro_mdom_1441, retro_mdom_1470, retro_mdom_1616, retro_mdom_1987, retro_mdom_903,
Otolemur garnettii	ENSOGAG00000011342	3 retrocopies	retro_ogar_2038, retro_ogar_265, retro_ogar_3453,
Procavia capensis	ENSPCAG00000000733	1 retrocopy	retro_pcap_386,
Sarcophilus harrisii	ENSSHAG00000013119	2 retrocopies	retro_shar_651, retro_shar_690,
Ictidomys tridecemlineatus	ENSSTOG00000008517	1 retrocopy	retro_itri_131,