RetrogeneDB ID: retro_mmul_2606

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:84661311..84662035(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMMUG00000015327
• Aliases: None
• Description: None

Sequence

>retro_mmul_2606
GAGGTAAACCAATATTTCATTTTCAAGATGGAAAATCAGTCAGACTCAGCTGTGGTTTTGCCTAGTACCACAGGCCTTTG
TGAATCCATCATCTCCCCATACAACTAGTTCATGAAAACAACCTATGAGTGCAACACTTAAAGAAAGATTAAGGAAAACA
AGTTCTTCATTTAATTCCTGTTACAATGTGATAAAACATCTTAAAGTAGAGAATGAAGAAAACAATAAGAACTTCTCAGA
GAAACCAACATCTTCCACAGAGGAAAACTGTTTGGAATTTCAAGAAAATTTTAAACACATAGTCAAGTGAATTTGAAAAA
AGCACATATTTGAAAAACACCTTCAAGAATATCCATGTGAGTGAATCTCAGTCACTTGATTCTGTGTCATGTAGTGTTCT
TCAAAATGAGTCTGTGAATTAGAATCTTCCTAAACAAGAATTAAATGAAGAAAAAGCAAATTTGGTGAAGCAGGTTCAGG
AGAAAGAAGACTTTCATTGGAGGCGAAATCTTGTCCAAATGTATAGATGAAAGAATGTTGATCAGTCTCAGTTACAGATG
TTAATAAAGAAATGGAGAAGCTGTAGCCAGCTGTTGATTTATGAGTTATAGTCAGCTATGTCTGAAGAGAACAAGAAACT
AAACCTACTCAACTGATAGACCACTATGGGTTAGACAATAAATTGCTACACTATAACAGAAGTGAAGAAGAATTTATAGG
TGTT

Alignment

ORF - retro_mmul_2606 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.47 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EKNQDFTFKMESSSDSAVVLPSTPQASANPSSPY-TNSSRKQPMSATLRERLRKTRSSFNSCYNVVKRLK
          E.NQ.F.FKME..SDSAVVLPST........SPY.T.S...QPMSATL.ERLRKT.SSFNSCYNV.K.LK
Retrocopy EVNQYFIFKMENQSDSAVVLPSTTGLCESIISPY>TSS*K-QPMSATLKERLRKTSSSFNSCYNVIKHLK

Parental  VESEENDQTFSDKPASSTEENCLEFQESFKHI-DSEFEENTNLKNTLKNLSVCESQSLHSGSCSALQNEF
          VE.EEN...FS.KP.SSTEENCLEFQE.FKHI..SEFE..T.LKNT.KN..V.ESQSL.S.SCS.LQNE.
Retrocopy VENEENNKNFSEKPTSSTEENCLEFQENFKHI>SSEFEKSTYLKNTFKNIHVSESQSLDSVSCSVLQNES

Parental  MNENLPKQRLNDEKAKLVKQVQEKEDLLRRLKLVKMYRSKN-DLSQLKVLIKKWRSCSQLLLYELQSAVS
          .N.NLPKQ.LN.EKA.LVKQVQEKED...R..LV.MYR.KN.D.SQL..LIKKWRSCSQLL.YEL.SA.S
Retrocopy VN*NLPKQELNEEKANLVKQVQEKEDFHWRRNLVQMYR*KNVDQSQLQMLIKKWRSCSQLLIYEL*SAMS

Parental  EENKKLSL-TQLIDHYGLDDKLLHYNRSEEEFIDV
          EENKKL.L.TQLIDHYGLD.KLLHYNRSEEEFI.V
Retrocopy EENKKLNL<TQLIDHYGLDNKLLHYNRSEEEFIGV

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	1.12 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.79 RPM
SRP007412_cerebellum	0.00 RPM	1.55 RPM
SRP007412_heart	0.00 RPM	0.94 RPM
SRP007412_kidney	0.00 RPM	0.59 RPM
SRP007412_liver	0.00 RPM	0.20 RPM
SRP007412_testis	0.00 RPM	9.69 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2606 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2606 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2606 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_3039

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000005386	2 retrocopies	retro_ecab_726, retro_ecab_887,
Echinops telfairi	ENSETEG00000015444	1 retrocopy	retro_etel_1418,
Gorilla gorilla	ENSGGOG00000025713	1 retrocopy	retro_ggor_3039,
Macaca mulatta	ENSMMUG00000015327	1 retrocopy	retro_mmul_2606 ,
Pteropus vampyrus	ENSPVAG00000004202	1 retrocopy	retro_pvam_742,