RetrogeneDB ID: retro_mmul_1698

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:92765743..92766543(-)
• Located in intron of: ENSMMUG00000002886

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB3IL1
• Ensembl ID: ENSMMUG00000015148
• Aliases: None
• Description: None

Sequence

>retro_mmul_1698
CTAGTGCAGGAGCTGGGGGAGCTGATGGCCAGCCTGTTTGAGGAAGCCCACAAGATGGTGTGGGAAGCCAACATGCAGTA
GGCAGTGTCAGAAACACAGCTGAATGAGGAGGCCTGGGGAAAGATAGCCATGTTGCAGGCAGAGATGACAGCGTGAAGAC
ACTGGTCATCATGTCCACACCAGCCTCTCCCAACTGCAAGCTCCACCTGCACCTGCTGAGCCCCATTAAGGGTGGGCCCC
GCAAGGCCCACTGCCAACATAGGAGCACCAGCAGTGCCTTCTCCTTGACCTTGTGCCCCACTGTGAGACATGCCCTCCCC
TTGGACAAGGAGGTGGATGTGACACTACTGGAAGAGTTCCAAGCCTGGAAGAAATTACCTACCCTGGACAAGACCTTTTC
CTTGCTGCAAAGGGTGTAGTGGGAGGACATGGGCCCTGCCTGGACTTCACAGTGCAGAATCTCTTGGCACTGGTGTAGGC
CTCTGTGGGGGACAACACACTCATCATCAAGACTGTGGCTCTGCAGAAGCTGCCTATAGTGAGGGTAACTGTGATCAGTT
GTGGCAGTGCCAATATGTATGTCTTGAGCAATTTGGCCCATACCTGCCACCACCACCACATCTGGCTTTGTGACTTTGAG
AGCCACTACCACATCTCACTGTCTTCTCAGGCCAGGATCACTGCAGTGTGCAACTTTTTTGTCTACATCTGCTACAACCA
CAAGGCCTGGTACAACAGGATTTGAAGCCAGTGTTCTGGGAGATCACAAAGCTGTGAAAGAGATACAGCTGGCCAAACTC

Alignment

ORF - retro_mmul_1698 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.82 %
• Parental protein coverage: 70.42 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LEQELEELTASLFEEAHKMVREANMKQAASEKQL-KEARGKIDMLQAEVTA-LKTLVITSTPASPNRELH
          L.QEL.EL.ASLFEEAHKMV.EANM..A.SE.QL..EA.GKI.MLQAE.TA..KTLVI.STPASPN..LH
Retrocopy LVQELGELMASLFEEAHKMVWEANMQ*AVSETQLNEEAWGKIAMLQAEMTA<VKTLVIMSTPASPNCKLH

Parental  PQLLSPTKAGPRKGHSRHKSTSSALCPAVCPAAGHTLTPDREGKEVDTILFAEFQAWREAPTLDKTCPFL
          ..LLSP.K.GPRK.H..H.STSSA.....CP...H.L..D...KEVD..L..EFQAW...PTLDKT...L
Retrocopy LHLLSPIKGGPRKAHCQHRSTSSAFSLTLCPTVRHALPLD---KEVDVTLLEEFQAWKKLPTLDKTFSLL

Parental  ERVHREDV-GPCLDFTMQELSTLVRAAVEDNTLTIEPVASQTLPAVKVAEVECSSTNTCALSGLTRTC-R
          .RV..ED..GPCLDFT.Q.L..LV.A.V.DNTL.I..VA.Q.LP.V.V....C.S.N...LS.L..TC..
Retrocopy QRV*WEDM<GPCLDFTVQNLLALV*ASVGDNTLIIKTVALQKLPIVRVTVISCGSANMYVLSNLAHTCHH

Parental  HRIRLGDSESHYYISPSSRARITAVCNFFTYIRYIQ-QGLVRQDAEPMFWEIMRL-RKEMSLAKL
          H.I.L.D.ESHY.IS.SS.ARITAVCNFF.YI.Y...QGLV.QD..P.FWEI..L..KE..LAKL
Retrocopy HHIWLCDFESHYHISLSSQARITAVCNFFVYICYNH<QGLVQQDLKPVFWEITKL<VKEIQLAKL

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	1.79 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	6.27 RPM
SRP007412_cerebellum	0.00 RPM	0.84 RPM
SRP007412_heart	0.00 RPM	4.59 RPM
SRP007412_kidney	0.12 RPM	23.24 RPM
SRP007412_liver	0.04 RPM	4.63 RPM
SRP007412_testis	0.00 RPM	118.96 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1698 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1698 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1698 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3716
Pan troglodytes	retro_ptro_2518
Pongo abelii	retro_pabe_3140

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000007376	1 retrocopy	retro_fcat_348,
Homo sapiens	ENSG00000167994	1 retrocopy	retro_hsap_3716,
Gorilla gorilla	ENSGGOG00000012399	1 retrocopy	retro_ggor_2513,
Macaca mulatta	ENSMMUG00000015148	1 retrocopy	retro_mmul_1698 ,
Nomascus leucogenys	ENSNLEG00000003273	1 retrocopy	retro_nleu_2858,
Pongo abelii	ENSPPYG00000003175	1 retrocopy	retro_pabe_3140,
Pan troglodytes	ENSPTRG00000003755	1 retrocopy	retro_ptro_2518,