RetrogeneDB ID: retro_mmul_1732

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:150122176..150123273(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MIPEP
• Ensembl ID: ENSMMUG00000006942
• Aliases: None
• Description: None

Sequence

>retro_mmul_1732
ATGGATTCCCTTGATCCAGAAACCAGGCAAGTGGCTGAACTGTTTATGTTTGATTTTGAAATTAGTGGAATCCATCTAGA
CAAAGAAAAGTGTAAAAGAGCAGTAGACCTCAATGTTAAAATCTTGGATTTGAGTAGTCCACATCTTATGGCAAACAACT
TTCCCAACAAGACCGAGAAGCATCTCTTACCAGAACACATTCGCCATAACTTTTATCTGATGGGGATCGTATCATAATTG
GTGGTCTCCATGCAGAAGCATGAGGTGACTTGGTGTGAGAAGCTGCTTACAAAATTTTTCTTTATCCCAATACTGGTCAA
TTAAAATGTTTAGAAGAATTGCTCAGCAACAGAGATCTTCTGGAAAAGTTGGTAGGTATTCTGTGTATTCCCACAGGGCT
CTCCAAGGAACAATAGTTAAAAATTCAGAGACTGTAGTCCAGTTCCTTGAGAAATTCTCTGACCAACTTTCTGAAAGAAC
TCTAAAAGATTTTGAGATGATATGAGGGATGAAAATGAAACAGAATTCTCAAAATTACAAAGTAATGCCTTGGGACCCCT
GCTATCACAGTGATGTGATTCATGAACACAGGTATAATATTGAGCCTGGCTTACATTGCCTGTTTTTCTCCCTTGGAGCA
TGCATGGAAGGCCTGAATATTTGGCTTAACAAACTGTTGGAGATTTCCTTATATGCAGAATAGCCTGCAAAAGGAGAGGT
ATGTGTGAAGATGTCCAAAAACTGGCTGTCATTCATGAATCTGAAGGATTGTTGGGGTGCATTTAACTTTGATTTTCTTC
AGCAAGCAGACAAACCACATCAGGATTGCCATTTTACAATCCATGGATGCAGATTAAAGGAAGACAGAGACTATTAACTC
CCAGTCATAGTTCTTATGCTGAATTTTCCCCATTCCTCAAGGAGTTCACCAACTTGGCTAACTTCTGGAATGAGGGAAAA
TCTTGTCCATGAAATGGGACATGCTATGCATTGAATGCTAGGATGTACTTGTTACCAACATGTCACCAGAACCAGGCTGT
CCCACTGATTTTGCAGAGGTTCCTTCTATTCTAATGGAGTACTTTACAAATGATTAT

Alignment

ORF - retro_mmul_1732 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.05 %
• Parental protein coverage: 51.33 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VDSLDPETRRVAELFMFDFEISGIHLDKEKRKRAVDLNVKILDLSSTFLMGTNFPNKIEKHLLPEHIRHN
          .DSLDPETR.VAELFMFDFEISGIHLDKEK.KRAVDLNVKILDLSS..LM..NFPNK.EKHLLPEHIRHN
Retrocopy MDSLDPETRQVAELFMFDFEISGIHLDKEKCKRAVDLNVKILDLSSPHLMANNFPNKTEKHLLPEHIRHN

Parental  F-TSAGDHIIIDGLHAEAPDDLVREAAYKIFLYPNAGQLKCLEELLSSRDLLAKLVG-YSTFSHRALQGT
          F..S.GD.III.GLHAEA..DLV.EAAYKIFLYPN.GQLKCLEELLS.RDLL.KLVG.YS..SHRALQGT
Retrocopy F<LSDGDRIIIGGLHAEA*GDLV*EAAYKIFLYPNTGQLKCLEELLSNRDLLEKLVG<YSVYSHRALQGT

Parental  IAKNPETVMQFLEKLSDKLSERTLKDFEMIREMKMKLNPQNSEVMPWDPPYYSGVIRAERYNIEPSLYCP
          I.KN.ETV.QFLEK.SD.LSERTLKDFEMI..MKMK.N.QN..VMPWDP.Y.S.VI...RYNIEP.L.C.
Retrocopy IVKNSETVVQFLEKFSDQLSERTLKDFEMI*GMKMKQNSQNYKVMPWDPCYHSDVIHEHRYNIEPGLHCL

Parental  FFSLGACMEGLNILLNRLLGISLYAEQPAKGEV-WSEDVRKLAVVHESEGLLGYI-YCDFFQRADKPHQD
          FFSLGACMEGLNI.LN.LL.ISLYAE.PAKGEV...EDV.KLAV.HESEGLLG.I...DF.Q.ADKPHQD
Retrocopy FFSLGACMEGLNIWLNKLLEISLYAE*PAKGEV<MCEDVQKLAVIHESEGLLGCI>NFDFLQQADKPHQD

Parental  CHFTIRGGRLKEDGDYQLPVVVLMLNLPRSSRSSPTLLTPGMMENLFHEMGHAMHSMLGRTRYQHVTGTR
          CHFTI.G.RLKED.DY.LPV.VLMLN.P.SSRSSPT.LT.GM.ENL.HEMGHAMH.MLG.T.YQHVT.TR
Retrocopy CHFTIHGCRLKEDRDY*LPVIVLMLNFPHSSRSSPTWLTSGMRENLVHEMGHAMH*MLGCTCYQHVTRTR

Parental  -CPTDFAEVPSILMEYFANDY
          .CPTDFAEVPSILMEYF.NDY
Retrocopy >CPTDFAEVPSILMEYFTNDY

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	18.49 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	18.40 RPM
SRP007412_cerebellum	0.00 RPM	12.40 RPM
SRP007412_heart	0.00 RPM	16.25 RPM
SRP007412_kidney	0.00 RPM	49.65 RPM
SRP007412_liver	0.00 RPM	23.20 RPM
SRP007412_testis	0.19 RPM	22.80 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1732 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1732 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1732 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3891
Gorilla gorilla	retro_ggor_2619
Pongo abelii	retro_pabe_3172

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000027001	1 retrocopy	retro_hsap_3891,
Gorilla gorilla	ENSGGOG00000009424	1 retrocopy	retro_ggor_2619,
Macaca mulatta	ENSMMUG00000006942	1 retrocopy	retro_mmul_1732 ,
Nomascus leucogenys	ENSNLEG00000013401	1 retrocopy	retro_nleu_1131,
Pongo abelii	ENSPPYG00000005207	1 retrocopy	retro_pabe_3172,
Sus scrofa	ENSSSCG00000009290	1 retrocopy	retro_sscr_415,
Sus scrofa	ENSSSCG00000025544	1 retrocopy	retro_sscr_414,