RetrogeneDB ID: retro_mmul_1813

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:1383532..1385120(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.12713
• Ensembl ID: ENSMMUG00000004984
• Aliases: None
• Description: None

Sequence

>retro_mmul_1813
TCTCTGCATGAGGGACCCCGAACCAGCTGGATCTGCTCATCTCGGGGGTGGAAGCATCTGTTCACAGCAGTAATGTACAC
GGTACAGAGAAGACAGTCGAAGCTGCCGAAGCCCTGCTTCATATGGAATCTCCTACCTGCTGGAGGGATTCGAGAAGTCC
TGTGGAAGTGTTTGTCCCTCCTTGTGTATCAGCTCCAGAATTTATCCATGCCACTATGAGGCCAGACGTCATTACCGAAA
CTGCAGTGGAGGCGTCGACGGAAGAGTCTGAACCAATGAGTACCTCTCCTATTCCTACATCACCAGATAGCTGTGAACCA
ATGAAAAAGAAAACAGTTGGCCGTAAACCAAAGACCCAGCAACCACCAGTTTCCAGTGGTCTTCTGAGTTAGGTACAATG
AAGAAACTGAGAGAAGGAAAAGGAAACAACCTATTTGTGGGAGTTTCTTTTAGATCTACTTCAAGATAAAAATACTTGTC
CCCGGTATATTAAATGGCCTCAGAGAGAAAAAGGCCTATTCAAGCTGGTGGATCCAAAAGCTATCTCTAAGCTTTGGGGA
AAGCATAAGAATAAACCAGACATGAACTATGAAACCATGGGACCAGCTTCAAGATACTACTACCAAAGGGGAATTCTTGC
AAAGGTTGCAGGACAGAGGCTTTGTATATCAGTTCAAGGATATGCCCCAAAACATAGTGGTCATAGACGATAACAAAAGT
GAAACCTGTAATGAAGATTTAGCAGGAGCTACAGATGAAAAATTATGAGAACGAGTGTCTCTGTCTGCAGAAAGTCTCCT
GAAAGCAGCATCCTCTGTTCGTGGTGGAAGAAATTCATCCCCTAGAAACTGCTCCAGAGCTGAGAAGGGTGAGGCTAGAT
TTGTGAATATCATTTCCCCTGGTCACCATGCTTCATCCAGGTCTCCTACTATCACTGCATCTGTATCAGCAACAGCAGCT
CCAAGGACCGTTTGTGTGGCAATGCAAGTACCTGTTGTAATGACATCATTGGGGCCAGAAAATTTCAGCTGTGGCAGTTC
AGTCACTTAATGCAGGTGCACCATTAATAATCAGCACGAGTCCAACAACAGCCACCTCTCCCAAGGCAGCCATTCAGGCA
GTCCCTGCTGTGATGCCAGCTTCTGCTGAAAACGGAGACAAAATCACCATGAAGCCTGCCAAAATTATTACCATCCCAGC
TACACAGCTTGCACAGTGTCAGCTGCAGACAAAGTCAAATCTGATTGGATCAGGAGGCATTCACACTGTTGGAGCCCCTT
TGGCTGTGAGAGCAGTTACCCCTGTTTCAATAGCCCCTGGTACACCTGTAATGAGACTGTCAGTGCCTACTCAGCAGGCA
TCTGGACAGACTCCTCCTCAAGTTACCAGTGTAGTCATAAAGGGACCGGAGGTTAAATCAGAAGCAATGGCATAAAAGCA
AGAATGTGATGTGGAAACTTTGCTGTTGGTAGAAGAAAAACTGGCAGATGGAAGTAAGACAGTGACCCATGTGGTGGTGG
TCAGTGCGCCTTCAGCTACTGCCCTTCCTGTAACTATGAAAACAGAAGAACTAGTGACATGTGAGAAA

Alignment

ORF - retro_mmul_1813 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.61 %
• Parental protein coverage: 99.44 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SLHEGPT-NQLDLLIRAVEASVHSSNAHCTDKTIEAAEALLHMESPTCLRDSRSPVEVFVPPCVSTPEFI
          SLHEGP..NQLDLLI..VEASVHSSN.H.T.KT.EAAEALLHMESPTC.RDSRSPVEVFVPPCVS.PEFI
Retrocopy SLHEGPR<NQLDLLISGVEASVHSSNVHGTEKTVEAAEALLHMESPTCWRDSRSPVEVFVPPCVSAPEFI

Parental  HAAMRPDVITETVVEVSTEESEPMDTSPIPTSPDSHEPMKKKKVGRKPKTQQSPISNGSPELGIKKKPRE
          HA.MRPDVITET.VE.STEESEPM.TSPIPTSPDS.EPMK.KK........Q.P...............E
Retrocopy HATMRPDVITETAVEASTEESEPMSTSPIPTSPDSCEPMK-KKTVGRKPKTQQPPVSSGLLS*VQ*RN*E

Parental  GKGNTTYLWEFLLDLLQDKNTCPRYIKWTQREKGIFKLVDSKAVSKLWGKHKNKPDMNYETMGRALRYYY
          ....TTYLWEFLLDLLQDKNTCPRYIKW.QREKG.FKLVD.KA.SKLWGKHKNKPDMNYETMG.A.RYYY
Retrocopy KEKETTYLWEFLLDLLQDKNTCPRYIKWPQREKGLFKLVDPKAISKLWGKHKNKPDMNYETMGPASRYYY

Parental  QRGILAKVEGQRL-VYQFKDMPKNIVVIDDDKSETCNEDLAGATDEKSLERVSLSAESLLKASSSVRSGK
          QRGILAKV.GQRL.VYQFKDMP.NIVVIDD.KSETCNEDLAGATDEK..ERVSLSAESLLKA.SSVR.G.
Retrocopy QRGILAKVAGQRL>VYQFKDMPQNIVVIDDNKSETCNEDLAGATDEKL*ERVSLSAESLLKAASSVRGGR

Parental  NSSPINCSRAEKGVARVVNITSPGHDASSRSPTTNASVSATAAPRTVRVAMQVPVVMTSLG-QKISTVAV
          NSSP.NCSRAEKG.AR.VNI.SPGH.ASSRSPT..ASVSATAAPRTV.VAMQVPVVMTSLG.QKIS.VAV
Retrocopy NSSPRNCSRAEKGEARFVNIISPGHHASSRSPTITASVSATAAPRTVCVAMQVPVVMTSLG>QKISAVAV

Parental  QSVNAGAPLITSTSPTTATSPKVVIQTIPTVMPASTENGDKITMQPAKIITIPATQLAQCQLQTKSNLTG
          QS.NAGAPLI.STSPTTATSPK..IQ..P.VMPAS.ENGDKITM.PAKIITIPATQLAQCQLQTKSNL.G
Retrocopy QSLNAGAPLIISTSPTTATSPKAAIQAVPAVMPASAENGDKITMKPAKIITIPATQLAQCQLQTKSNLIG

Parental  SGSINIVGTPLAVRALTPVSIAHGTPVMRLSMPTQQASGQTPPRVISAVIKGPEVKSEAVAKKQEHDVKT
          SG.I..VG.PLAVRA.TPVSIA.GTPVMRLS.PTQQASGQTPP.V.S.VIKGPEVKSEA.A.KQE.DV.T
Retrocopy SGGIHTVGAPLAVRAVTPVSIAPGTPVMRLSVPTQQASGQTPPQVTSVVIKGPEVKSEAMA*KQECDVET

Parental  LQLVEEKPADGNKTVTHVVVVSAPSAIALPVTMKTEGLVTCEK
          L.LVEEK.ADG.KTVTHVVVVSAPSA.ALPVTMKTE.LVTCEK
Retrocopy LLLVEEKLADGSKTVTHVVVVSAPSATALPVTMKTEELVTCEK

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	23.87 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	11.98 RPM
SRP007412_cerebellum	0.00 RPM	29.51 RPM
SRP007412_heart	0.06 RPM	23.61 RPM
SRP007412_kidney	0.00 RPM	25.23 RPM
SRP007412_liver	0.00 RPM	15.16 RPM
SRP007412_testis	0.34 RPM	101.73 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1813 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1813 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1813 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003174	1 retrocopy	retro_cjac_540,
Homo sapiens	ENSG00000109381	1 retrocopy	retro_hsap_3546,
Macaca mulatta	ENSMMUG00000004984	1 retrocopy	retro_mmul_1813 ,
Pongo abelii	ENSPPYG00000015068	1 retrocopy	retro_pabe_2929,
Pan troglodytes	ENSPTRG00000016449	1 retrocopy	retro_ptro_2410,