RetrogeneDB ID: retro_mmul_2365

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:106075495..106075792(-)
• Located in intron of: ENSMMUG00000019407

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED21
• Ensembl ID: ENSMMUG00000003218
• Aliases: None
• Description: mediator of RNA polymerase II transcription subunit 21 [Source:RefSeq peptide;Acc:NP_001245049]

Sequence

>retro_mmul_2365
GATCAGCTCATGCAGCTGTAAGACACCATGAACTCACTTTCAGATCAGTTTTGTAATGCCACTGATGTGTTGCAGCAATG
TGGTCTTCCTGCCTCTTTTAATAATATTCAGACAGCAATTAACAAAGACCAGCCAGCTAACCCTACAGAAGAGTATGCTC
AGCTTCTTACAGCACTGATTGCACAAACAGCAAAAGACATTGATGTTTTGATAGACTCCTTATCCAGTGAAGAATCTACA
GCTGCTTTATAGGCTACTAGCTTATATAAGCTACAGTAAAACCATGAGGCTGCTACA

Alignment

ORF - retro_mmul_2365 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81. %
• Parental protein coverage: 69.44 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DRLTQLQDAVNSLADQFCNAIGVLQQCGPPASFSNIQTAINKDQPANPTEEYAQLFAALIARTAKDIDVL
          D.L.QL.D..NSL.DQFCNA..VLQQCG.PASF.NIQTAINKDQPANPTEEYAQL..ALIA.TAKDIDVL
Retrocopy DQLMQL*DTMNSLSDQFCNATDVLQQCGLPASFNNIQTAINKDQPANPTEEYAQLLTALIAQTAKDIDVL

Parental  IDSLPSEESTAALQAASLYKLEEENHEAAT
          IDSL.SEESTAAL.A.SLYKL...NHEAAT
Retrocopy IDSLSSEESTAAL*ATSLYKL-Q*NHEAAT

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	18.71 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	14.04 RPM
SRP007412_cerebellum	0.06 RPM	21.37 RPM
SRP007412_heart	0.00 RPM	16.49 RPM
SRP007412_kidney	0.00 RPM	22.65 RPM
SRP007412_liver	0.00 RPM	6.14 RPM
SRP007412_testis	0.00 RPM	39.58 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2365 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2365 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2365 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4105
Pan troglodytes	retro_ptro_2786
Gorilla gorilla	retro_ggor_2756
Pongo abelii	retro_pabe_3361

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011670	1 retrocopy	retro_amel_108,
Dasypus novemcinctus	ENSDNOG00000010041	1 retrocopy	retro_dnov_998,
Homo sapiens	ENSG00000152944	1 retrocopy	retro_hsap_4105,
Gorilla gorilla	ENSGGOG00000016313	1 retrocopy	retro_ggor_2756,
Myotis lucifugus	ENSMLUG00000007678	1 retrocopy	retro_mluc_229,
Macaca mulatta	ENSMMUG00000003218	1 retrocopy	retro_mmul_2365 ,
Pongo abelii	ENSPPYG00000004377	1 retrocopy	retro_pabe_3361,
Pan troglodytes	ENSPTRG00000004785	1 retrocopy	retro_ptro_2786,
Pteropus vampyrus	ENSPVAG00000013357	1 retrocopy	retro_pvam_449,
Ictidomys tridecemlineatus	ENSSTOG00000008391	2 retrocopies	retro_itri_1005, retro_itri_1057,