RetrogeneDB ID: retro_mmul_2479

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:22186850..22188353(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUPT20H
• Ensembl ID: ENSMMUG00000003590
• Aliases: None
• Description: suppressor of Ty 20 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:20596]

Sequence

>retro_mmul_2479
ATGGATAGAGATTTAGAACAGGCTCTGGATCGCGCAGAGAATATCATTGAAATTGCCCAACAGAGACCTCCTAGAAGGAG
ATACTCACCTAGGGCGGGAAAAACTCTGCAGGAAAAACTTTATGACATTTATGTAGAAGAATGTGGAAAAGAGCCTGAGG
ATCCTCAGGAATTGAGAAGCAATGTAAACTTGTTAGAAAAGCTTGTTAGGAGAGAGTCCTTGCCATGTTTACTGGTCAAT
CTATACCCAGGCAATCAGGGGTATTCTGTGATGCTCCAGAGAAAAGATGGGTCCTTTGCAGAGACCATTCGACTCCCTTA
TGATGAGAGGGCATTGCTCGACTACTTGGATGCAGAAGAATTACCCCCTGCTTTGGCTGATGTCCTTGATAAAGCTTCGG
TTAACATTTTTCATAGTGGGTGTGTCATAGTAGAAGTTCGTGACTACAGGCAGTCCAGTAATATGCAACCTCCTGGTTAC
CAAAGCAGGCATATTCTCCTACGTCCAACAATGCAGACTTTAGCCCATGATGTGAAGATGATGACAAGAGATGTCCAGAA
ATGGAGCCAGGAAGACAAGCTGCAGCTTGAGAGCCAACTGATCTTAGCGACAGCTGAACCACTGTGTCTCGATCCTTCTG
TAGCAGTCGCCTGCACTGCAAACAGGCTGCTGTACAACAAGCAAAAGATGAATACCGACCCGATGAAACGGTGCCTCCAG
AGGTATTCGTGGCCCTCTGTAAGGTCACAGCAGGAGCGGTCTGACTATCCACCTCCTCCTGAGATGAGAGTGTCGACTTC
TGGCCAAAAAGAAGAAAGAAAAGCAGGTCAGCCTTATGAGCTGGACATTGCTAAAGCAGGACGTTGTGTAGACATGTGGA
AACGCAGATCCTGGGATTTGGCCGTGCCTTCGGAAGTGGATGTGGAGAAACTTGCTAAAGAGTGTCAGCCCGTCACAGCT
GCTGAGCCACAGCTCCCAGTCTGGCCAGCCCAGGAGGTAGAAGACCCTTTCAGATTTGGATGGGAAGCTGGCTCTCAGGC
CTGGGACACCAAGCCAAGCATCATGCAGTCGTTTAATGATCCACTTCTCTGTGGTAAAATACGGCCCCGTAAAAAAGCCA
GGCAGAAGAGCCAGAAGTCTCCCTGGCAGCCCTTCCCAGATGACCATGCAGCTGGTCTCAGGCCTGGGTCAGAGACTGAT
GCTGGGAGGGCAGTGAGTCAGGCCCAGGAATCAGTGCAGAGCAGAGTCAAAGGTCCAGGCAAGATGCCACACAGCTCCAG
TGGCCCAGCCAGTGTCAGTCAGCTCTCTTCATGGAAAACACCAGAACAGCCTAAGCCTGTGTGGGTCCAGTCTTCAGTAT
TGGGGAAAGGAGAGAAATATCCACCTCCCCGAAACCAACTTCCCTCAAGCTCAGGAAAGAATTCCTCAGGTACCAGTTTT
CCCCCACAACAGGCAGGCAGCTCTCTTAAGCGTCCTTTTCCTGCTGCTGCTGCCGCTCCTGCG

Alignment

ORF - retro_mmul_2479 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.23 %
• Parental protein coverage: 94.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQQALELALDRAEYVIESARQRPPKRKYLSSGRKSVFQKLYDLYIEECEKEPE-VKKLRRNVNLLEKLVM
          M...LE.ALDRAE..IE.A.QRPP.R.Y.....K....KLYD.Y.EEC.KEPE....LR.NVNLLEKLV.
Retrocopy MDRDLEQALDRAENIIEIAQQRPPRRRYSPRAGKTLQEKLYDIYVEECGKEPEDPQELRSNVNLLEKLVR

Parental  QETLSCLVVNLYPGNEGYSLMLRGKNGSDSETIRLPYEEGELLEYLDAEELPPILVDLLEKSQVNIFHCG
          .E.L.CL.VNLYPGN.GYS.ML..K.GS..ETIRLPY.E..LL.YLDAEELPP.L.D.L.K..VNIFH.G
Retrocopy RESLPCLLVNLYPGNQGYSVMLQRKDGSFAETIRLPYDERALLDYLDAEELPPALADVLDKASVNIFHSG

Parental  CVIAEIRDYRQSSNMKSPGYQSRHILLRPTMQTLICDVHSITSDNHKWTQEDKLLLESQLILATAEPLCL
          CVI.E.RDYRQSSNM..PGYQSRHILLRPTMQTL..DV...T.D..KW.QEDKL.LESQLILATAEPLCL
Retrocopy CVIVEVRDYRQSSNMQPPGYQSRHILLRPTMQTLAHDVKMMTRDVQKWSQEDKLQLESQLILATAEPLCL

Parental  DPSIAVTCTANRLLYNKQKMNTRPMKRCFKRYSRSSLNRQQDLSHCPPPPQLRLLDFLQKRKERKAGQHY
          DPS.AV.CTANRLLYNKQKMNT.PMKRC..RYS..S...QQ..S..PPPP..R.....QK..ERKAGQ.Y
Retrocopy DPSVAVACTANRLLYNKQKMNTDPMKRCLQRYSWPSVRSQQERSDYPPPPEMRVSTSGQK-EERKAGQPY

Parental  DLKISKAGNCVDMWKRSPCNLAIPSEVDVEKYAKVEKSIKSDDSQPTVWPAHDVKDDYVFECETGTQYQK
          .L.I.KAG.CVDMWKR....LA.PSEVDVEK.AK..........Q..VWPA..V.D...F..E.G.Q...
Retrocopy ELDIAKAGRCVDMWKRRSWDLAVPSEVDVEKLAKECQPVTAAEPQLPVWPAQEVEDPFRFGWEAGSQAWD

Parental  TKLTILQSLGDPLYYGKIQPCKADEESDSQMSPSHSSTDDHSNWFVIGSKTDAERVVNQYQELVQNEAKC
          TK..I.QS..DPL..GKI.P.K......SQ.SP.....DDH......GS.TDA.R.V.Q.QE.VQ...K.
Retrocopy TKPSIMQSFNDPLLCGKIRPRKKARQK-SQKSPWQPFPDDHAAGLRPGSETDAGRAVSQAQESVQSRVKG

Parental  PVKMSHSSSGSASLSQVSPGKETEQTETVSVQSSVLGKGVKHRPPPIKLPSSSGNSSSGNYFTPQQTSSF
          P.KM.HSSSG.AS.SQ.S..K..EQ...V.VQSSVLGKG.K..PP...LPSSSG..SSG..F.PQQ..S.
Retrocopy PGKMPHSSSGPASVSQLSSWKTPEQPKPVWVQSSVLGKGEKYPPPRNQLPSSSGKNSSGTSFPPQQAGSS

Parental  LKSPTPPPSSKPS
          LK.P.P.....P.
Retrocopy LKRPFPAAAAAPA

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	33.50 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	26.18 RPM
SRP007412_cerebellum	0.00 RPM	56.50 RPM
SRP007412_heart	0.00 RPM	17.67 RPM
SRP007412_kidney	0.00 RPM	38.14 RPM
SRP007412_liver	0.00 RPM	13.46 RPM
SRP007412_testis	0.60 RPM	126.76 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2479 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2479 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2479 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4659
Pan troglodytes	retro_ptro_3095
Pongo abelii	retro_pabe_3619
Equus caballus	retro_ecab_1052

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000000116	2 retrocopies	retro_ecab_1052, retro_ecab_1101,
Homo sapiens	ENSG00000102710	2 retrocopies	retro_hsap_4659, retro_hsap_4794,
Loxodonta africana	ENSLAFG00000027507	1 retrocopy	retro_lafr_1199,
Macaca mulatta	ENSMMUG00000003590	2 retrocopies	retro_mmul_2479 , retro_mmul_2555,
Pongo abelii	ENSPPYG00000005288	2 retrocopies	retro_pabe_3619, retro_pabe_3729,
Pan troglodytes	ENSPTRG00000005791	2 retrocopies	retro_ptro_3095, retro_ptro_3189,
Pteropus vampyrus	ENSPVAG00000014609	1 retrocopy	retro_pvam_401,
Tarsius syrichta	ENSTSYG00000013227	1 retrocopy	retro_tsyr_2160,
Vicugna pacos	ENSVPAG00000007288	1 retrocopy	retro_vpac_193,