RetrogeneDB ID: retro_mmul_240

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:76401453..76402599(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000018977
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMMUG00000007870
• Aliases: None
• Description: None

Sequence

>retro_mmul_240
ATGCCCTTCTCCAACAGCCACAACGCGCTGAAGCTGCGCTTCCCCGCCGAGGACGAGTTCCCGGACCTGAGCGCCCACAA
CAACCACATGGCCAAGGTGCTGACCCCCGAGCTGTACGCGGAGCTGCGCGCCAAGAGCACGCCGAGCGGCTTCACGCTGG
ACGACGTCATCCAGACAGGCGTGGACAACCCGGGCCACCCGTACATCATGACCGTGGGCTGCGTGGCGGGCGACGAGGAG
TCCTACGACGTGTTCAAGGATCTCTTCGACCCCATCATCGAGGACCGGCACGGCGGCTACAAGCCCAGCGATGAGCACAA
GACCGACCTCAACCCCGACAACCTGCAGGGCGGCGACGACCTGGACCCCAACTACGTGCTGAGCTCGCGGGTGCGCACGG
GCCGCAGCATCCGCGGCTTCTGCCTGCCCCCGCACTGCAGCCGCGGGGAGCGCCGCGCCATCGAGAAGCTCGCGGTGGAA
GCCCTGTCCAGCCTGGACGGCGACCTGGCGGGCCGGTACTACGCGCTCAAGAGCATGACGGAGGCGGAGCAGCAGCAGCT
CATCGACGACCACTTCCTCTTCGACAAGCCCGTGTCACCTCTGCTGCTGGCCTCGGGCATGGCCCGCGACTGGCCCGACG
CCCGCGGTATCTGGCACAATGACAATAAGACCTTCCTGGTGTGGGTCAACGAGGAGGATCACCTGCGGGTCATCTCCATG
CAGAAGGGGGGCAACATGAAGGAGGTGTTCACCCGCTTCTGCACCGGCCTCACCCAGATTGAAACTCTCTTCAAGTCTAA
GAACTATGAGTTCATGTGGAACCCTCACCTGGGCTACATCCTCACCTGCCCATCCAACCTGGGCACAGGGCTGCGGGCAG
GAGTGCACATCAAGCTGCCCCACCTGGGCAAGCATGAGAAGTTCTCGGAGGTGCTTAAGCGGCTACGACTTCAGAAGCGA
GGCACAGGCGGTGTGGACACGGCTGCAGTGGGCGGGGTCTTCGACGTCTCCAACGCTGACCGCCTGGGCTTCTCGGAGGT
GGAGCTGGTGCAGATGGTGGTGGACGGAGTGAAGCTGCTCATCGAGATGGAGCAGCGGCTGGAGCAGGGCCAGGCCATCG
ACGACCTCATGCCTGCCCAGAAGTGA

Alignment

ORF - retro_mmul_240 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.53 %
• Parental protein coverage: 87.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YPPSAEYPDLRKHNNCMASHLTPAVYARLCDKTTPTGWTLDQCIQTGVDNPGHPFIKTVGMVAGDEETYE
          .P...E.PDL..HNN.MA..LTP..YA.L..K.TP.G.TLD..IQTGVDNPGHP.I.TVG.VAGDEE.Y.
Retrocopy FPAEDEFPDLSAHNNHMAKVLTPELYAELRAKSTPSGFTLDDVIQTGVDNPGHPYIMTVGCVAGDEESYD

Parental  VFADLFDPVIQERHNGYDPRTMKHTTDLDASKIRSG-YFDERYVLSSRVRTGRSIRGLSLPPACTRAERR
          VF.DLFDP.I..RH.GY.P....H.TDL.......G...D..YVLSSRVRTGRSIRG..LPP.C.R.ERR
Retrocopy VFKDLFDPIIEDRHGGYKP-SDEHKTDLNPDNLQGGDDLDPNYVLSSRVRTGRSIRGFCLPPHCSRGERR

Parental  EVERVVVDALSGLKGDLAGRYYRLSEMTEAEQQQLIDDHFLFDKPVSPLLTAAGMARDWPDARGIWHNNE
          ..E...V.ALS.L.GDLAGRYY.L..MTEAEQQQLIDDHFLFDKPVSPLL.A.GMARDWPDARGIWHN..
Retrocopy AIEKLAVEALSSLDGDLAGRYYALKSMTEAEQQQLIDDHFLFDKPVSPLLLASGMARDWPDARGIWHNDN

Parental  KSFLIWVNEEDHTRVISMEKGGNMKRVFERFCRGLKEVEQLIQERGWEFMWNERLGYILTCPSNLGTGLR
          K.FL.WVNEEDH.RVISM.KGGNMK.VF.RFC.GL...E.L......EFMWN..LGYILTCPSNLGTGLR
Retrocopy KTFLVWVNEEDHLRVISMQKGGNMKEVFTRFCTGLTQIETLFKSKNYEFMWNPHLGYILTCPSNLGTGLR

Parental  AGVHIKLPLLSKDSRFPKILENLRLQKRGTGGVDTAATGGVFDISNLDRLGKSEVELVQLVIDGVNYLID
          AGVHIKLP.L.K...F...L..LRLQKRGTGGVDTAA.GGVFD.SN.DRLG.SEVELVQ.V.DGV..LI.
Retrocopy AGVHIKLPHLGKHEKFSEVLKRLRLQKRGTGGVDTAAVGGVFDVSNADRLGFSEVELVQMVVDGVKLLIE

Parental  CERRLERGQDI
          .E.RLE.GQ.I
Retrocopy MEQRLEQGQAI

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	127.40 RPM	179.50 RPM
SRP007412_brain_prefrontal_cortex	886.83 RPM	173.73 RPM
SRP007412_cerebellum	114.62 RPM	304.92 RPM
SRP007412_heart	39.98 RPM	0.82 RPM
SRP007412_kidney	40.26 RPM	31.92 RPM
SRP007412_liver	8.83 RPM	0.51 RPM
SRP007412_testis	11.27 RPM	2.53 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_240 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_240 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_240 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000019748	2 retrocopies	retro_etel_1343, retro_etel_2075,
Macaca mulatta	ENSMMUG00000007870	1 retrocopy	retro_mmul_240 ,
Tupaia belangeri	ENSTBEG00000012104	1 retrocopy	retro_tbel_4,
Tursiops truncatus	ENSTTRG00000005837	1 retrocopy	retro_ttru_1863,