RetrogeneDB ID: retro_mmul_2555

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:22141406..22142888(-)
• 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_2555
ATGGATCGAGATTTAGAACAGGCTCTGAATGGCGCAGAGAATATCATTGAAATTGCCCAACAGAGACCTCCTAGAAGGAG
ATACTCACCTAGGGCGGGAAAATCTCTGCAGGAAAAACTTTATGACATTTATATAGAAGAATGTGGAAAAGAGCCTGAGG
ATCCTCAGGAATTGAGAAGCAATGTAAACTTGTTAGAAAAGCTTGTTAGGAGAGAGTCCTTGCCATGTTTACTGGTCAAT
CTATACCCAGGCAATCAGGGGTATTCTGTGATGCTCCAGAGAAAAGATGGGTCCTTTGCAGAGACCATTCCGCTGCCTTA
TGATGAAAGGACATTGCTCGACTACTTGGATGCAGAAGAATTACCCCCTGCTTTGGCTGATGTCCTTGATAAAGCTTCGG
TTAACATTTTTCATAGTGGGTGTGTCATAGTAGAAGTTCGTGACTACAGGCAGTCCAGTAATATGCAACCTTCTGGTTAC
CAAAGCAGGCATATTCTCCTACATTCAGCGATGCCGACTTTAGCCCATGAGGTGAATACAATGACAAGAGATGTCCAGAA
ATGGAGCCAGGAAGACAAATTTCCACTTGAGAGTCAACTGATCTTAGAGACAGCTGAACCACTGTATCTCGATCCTTCTG
TAGCAGTCTCCTGTTCTGCAAACAGGCTGCTGTATAACAAGCAAAAGATGAATACCGACCCGATGAAACGGTGCCTCCAG
AGGTATTCGTGGCCTTCTGTAAGGTCACAGCAGGAGCGGTCTGACTATCCACCTCCTCCTGAGATGAGAATTTCGACTTC
TGGCCAAAAAGAAAAAAGAAAAGCAGGTCAGCCTTATGAGCTGGACATTGCTAAAGCAGGACGTTGTGTTGACATGTGGA
AACGCAGATCCTGGGATTTGGCCGTGCCTTCGGAAGTGGATGTGGAGAAACTTGCTAAAGGGTGTCAGCCCGTCACAGCT
GCTGACCCACAGCTCCCAGTCTGGCCAGCCCAGGAGGTAGAAGACCCTTTCGGATTTGGATGGGAAGCTGGCTCTCAGGC
CTGGGACACCAAGCCAAACATCATGCAGTCGTTTAATGATCCGTTTTTCAGTGGTGAAATAGGGCCCCGTAAAAAAGCCA
GGCAGAAGAGCCAGAAGTCTCCCTGGCAGCCCTTCCCAGATGACCATGCAGCTGGTCTCAGGCCTGGGTCAGAGACTGAT
GCTGGGAGGGCAGTGAGTCAGGCCCAGGAATCGGTGCAGAGCAGAGTCAAAGGTCCAGGCAAGATGCCACACAGCTCCAG
TGGCCCAGCCAGTGTCAGTCAGCTCTCTTCATGGAAAACACCAGAACAGCCTAAGCCTGTGTGGGTCCAGTCTTCAGTAT
TGGGGAGGAGAGAGAAACATCCACCTCCCCGAAACCAACTTCCCTCAAGCTCAGGAAAGAATTCCTCAGGTACCAGTTTT
CCCCCACAACAGGCAGGCAGCTCTCTTAAGCGTCCTTTTCCT

Alignment

ORF - retro_mmul_2555 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.86 %
• Parental protein coverage: 92.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQQALELALDRAEYVIESARQRPPKRKYLSSGRKSVFQKLYDLYIEECEKEPE-VKKLRRNVNLLEKLVM
          M...LE.AL..AE..IE.A.QRPP.R.Y.....KS...KLYD.YIEEC.KEPE....LR.NVNLLEKLV.
Retrocopy MDRDLEQALNGAENIIEIAQQRPPRRRYSPRAGKSLQEKLYDIYIEECGKEPEDPQELRSNVNLLEKLVR

Parental  QETLSCLVVNLYPGNEGYSLMLRGKNGSDSETIRLPYEEGELLEYLDAEELPPILVDLLEKSQVNIFHCG
          .E.L.CL.VNLYPGN.GYS.ML..K.GS..ETI.LPY.E..LL.YLDAEELPP.L.D.L.K..VNIFH.G
Retrocopy RESLPCLLVNLYPGNQGYSVMLQRKDGSFAETIPLPYDERTLLDYLDAEELPPALADVLDKASVNIFHSG

Parental  CVIAEIRDYRQSSNMKSPGYQSRHILLRPTMQTLICDVHSITSDNHKWTQEDKLLLESQLILATAEPLCL
          CVI.E.RDYRQSSNM...GYQSRHILL...M.TL...V...T.D..KW.QEDK..LESQLIL.TAEPL.L
Retrocopy CVIVEVRDYRQSSNMQPSGYQSRHILLHSAMPTLAHEVNTMTRDVQKWSQEDKFPLESQLILETAEPLYL

Parental  DPSIAVTCTANRLLYNKQKMNTRPMKRCFKRYSRSSLNRQQDLSHCPPPPQLRLLDFLQKRKERKAGQHY
          DPS.AV.C.ANRLLYNKQKMNT.PMKRC..RYS..S...QQ..S..P.PP...............AGQ.Y
Retrocopy DPSVAVSCSANRLLYNKQKMNTDPMKRCLQRYSWPSVRSQQERSDYP-PPPEMRISTSGXXXXXXAGQPY

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

Parental  TKLTILQSLGDPLYYGKIQPCKADEESDSQMSPSHSSTDDHSNWFVIGSKTDAERVVNQYQELVQNEAKC
          TK..I.QS..DP...G.I.P.K......SQ.SP.....DDH......GS.TDA.R.V.Q.QE.VQ...K.
Retrocopy TKPNIMQSFNDPFFSGEIGPRKKARQK-SQKSPWQPFPDDHAAGLRPGSETDAGRAVSQAQESVQSRVKG

Parental  PVKMSHSSSGSASLSQVSPGKETEQTETVSVQSSVLGKGVKHRPPPIKLPSSSGNSSSGNYFTPQQTSSF
          P.KM.HSSSG.AS.SQ.S..K..EQ...V.VQSSVLG...KH.PP...LPSSSG..SSG..F.PQQ..S.
Retrocopy PGKMPHSSSGPASVSQLSSWKTPEQPKPVWVQSSVLGRREKHPPPRNQLPSSSGKNSSGTSFPPQQAGSS

Parental  LKSPTP
          LK.P.P
Retrocopy LKRPFP

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	0.11 RPM	33.50 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	26.18 RPM
SRP007412_cerebellum	0.00 RPM	56.50 RPM
SRP007412_heart	0.41 RPM	17.67 RPM
SRP007412_kidney	0.00 RPM	38.14 RPM
SRP007412_liver	0.00 RPM	13.46 RPM
SRP007412_testis	1.32 RPM	126.76 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2555 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2555 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2555 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4794
Pan troglodytes	retro_ptro_3189
Pongo abelii	retro_pabe_3729
Equus caballus	retro_ecab_1101

---

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,