RetrogeneDB ID: retro_mmul_406

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:120524747..120525182(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS25
• Ensembl ID: ENSMMUG00000002149
• Aliases: None
• Description: None

Sequence

>retro_mmul_406
ATGGTGATGAATTTCAAGTGTTTGTGGCAGTATCGCTTCCCGCCCTTTATATTACAGCTGAACATGGCCACTTGGCAGAA
GCAGCTGGCCACCTGGTGTTCGTTGGTTCTGTCCATCTGCTGCCTACACAAACAGTCCAGTGTGATGGCGGTGGATGCTC
AGGAGATCCTGCTCTTCAGCACCGTCAAGCTGTGGAAGCTTCCTGTGGGATCAGTCCAGGTTGTATTAGAGGAACTAAGG
AAGAATGGGAACTTACAGTGGCTGGATAAGAGCAAGTCTAGCTTCCTAATCGTGTGGCAGAGGCCAGAAGAATGGGGGAA
ACTCATCTATCAGTGGGTCTCCAGGAGTGGCCAGAACAACTCCATACTTAGCCTGTATGAGCTGACCAACAGGGAAAACA
TAGAGAATAAGTTGTTCCATGGACTAAAGGAGGCC

Alignment

ORF - retro_mmul_406 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 83.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAMSFEWPWQYRFPPFFTLQPNVDTRQKQLAAWCSLVLSFCRLHKQSSMTVMEAQESPLFNNVKLQRKLP
          M.M.F...WQYRFPPF..LQ.N..T.QKQLA.WCSLVLS.C.LHKQSS.....AQE..LF..VKL..KLP
Retrocopy MVMNFKCLWQYRFPPFI-LQLNMATWQKQLATWCSLVLSICCLHKQSSVMAVDAQEILLFSTVKLW-KLP

Parental  VESIQIVLEELRKKGNLEWLDKSKSSFLIMWRRPEEWGKLIYQWVSRSGQNNSVFTLYELTNGEDTEDEE
          V.S.Q.VLEELRK.GNL.WLDKSKSSFLI.W.RPEEWGKLIYQWVSRSGQNNS...LYELTN.E..E...
Retrocopy VGSVQVVLEELRKNGNLQWLDKSKSSFLIVWQRPEEWGKLIYQWVSRSGQNNSILSLYELTNRENIENKL

Parental  FHGLDEA
          FHGL.EA
Retrocopy FHGLKEA

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	15.24 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	19.36 RPM
SRP007412_cerebellum	0.00 RPM	14.66 RPM
SRP007412_heart	0.00 RPM	13.66 RPM
SRP007412_kidney	0.00 RPM	37.79 RPM
SRP007412_liver	0.00 RPM	36.73 RPM
SRP007412_testis	0.00 RPM	17.60 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_406 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_406 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_406 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_213
Pan troglodytes	retro_ptro_334
Gorilla gorilla	retro_ggor_284
Pongo abelii	retro_pabe_427

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013276	1 retrocopy	retro_cjac_2959,
Homo sapiens	ENSG00000131475	1 retrocopy	retro_hsap_213,
Gorilla gorilla	ENSGGOG00000016041	1 retrocopy	retro_ggor_284,
Macropus eugenii	ENSMEUG00000011611	2 retrocopies	retro_meug_1247, retro_meug_1681,
Macaca mulatta	ENSMMUG00000002149	1 retrocopy	retro_mmul_406 ,
Nomascus leucogenys	ENSNLEG00000011797	1 retrocopy	retro_nleu_1862,
Ochotona princeps	ENSOPRG00000012574	1 retrocopy	retro_opri_1071,
Pongo abelii	ENSPPYG00000008377	1 retrocopy	retro_pabe_427,
Pan troglodytes	ENSPTRG00000009220	2 retrocopies	retro_ptro_1624, retro_ptro_334,