RetrogeneDB ID: retro_mmul_2583

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:55757637..55759629(-)
• Located in intron of: ENSMMUG00000016725

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.11181
• Ensembl ID: ENSMMUG00000001319
• Aliases: None
• Description: None

Sequence

>retro_mmul_2583
CCTGTTCCTGGTAGCTTAAGGCCCATGATGGTTGCAATGCTCATACAGAGCACAGTAGAGAGTACCAAGTGTTTCCTGGA
GAAATTTAAGCCAGGAAAGTGGATGAATCAGTATAACAACCTTAACTTCAAGACACTTGTTCCAAGTGATATTGATATAT
CACGATCTTGTAAACTGAAGCCCATTGGTAAGCTGGCTCGAGAAATTGGTCTGCTGTCTGAAGAGGTAGAATTATATGGT
GAAACAAAGGCCAAAGTTCTGCTGTCAGCACTAGAACACCTGAAGCACCAGCCTGATGGGAAATACCGGGTGGTGACTGG
AATAACCCCAACACTCCGGGAGAAGGGAAAAGCACGACTACAATCGGGCTGGTGCAAGCCCTTTTTGCCCATATCTACCA
GAACATTTTTGTGTGTGCGACAGCCTTCTCAGGGCCCCATCTTTGGAATAAAAGGTGGTGCCGCAGGAGGTGGCTACTCC
CAGATCATTCCTATGGAATAGTTTAATCTCCACCTCACAGGTGACATCCATGCCATCACTGTAGCTAATAACCTCATTGC
TGCGGCCATTGATGCTCAGATATTTCATGAACTGCCCCAGACAGACAAGGCTCTCTTTAATCGTTTGGTGCTATCAGTAA
ATGGAGTGAGAAAGTTCTCTGATATCCACATCCGAAGGTTAAATAGACTAGGCATTGAAAAGACTGACCCTACCACACTG
ACAGATGAAGAGATAAACAGATTTGTAAGATTGGACATTGATCCAGATATCAAAACTTGGCAAAGAGTGTTGGATACCAA
TGATAGATTCCTGAGGAAGATCATGATTGGACAGGCTCCAACAAAGAAAGGTCACATAAGGACGGCCCAGTTTGATATCT
CTGTGGCCAGTGAAATTATGGCTGTCCTGGCTCTCACCACTTCTCTAGAAGATATGAGAGAGAGACTGGGCAAAATGGGG
GTGGCATCCAGTAAGAAAGGAGAGCCCATCCGCGCTGAAGATCTGGGGGTGGGTGGTGCATTGATAGTGCTTATGAAGGA
CGCAATCAAGCCCAATCTTATGCAGACATTGGAGGGCACTCCAGTGCCGTTTGTCCATGCCGGCCCATTTGCCAACATCG
CACATGGCAATTCCCCTATCATTGCAGACCGATCGCACTCAAGCTTGTTGGCCCAGAAGGGTTTGCAGTGACGGAAGTGG
GATTTGGAGCAGACATTGGAATGGAAAAATTTTTTAACATCAAATCCCGGTATTCCGGCCTCCACCCTCACGTGGTGGTG
CTTGTTGACACTGTCAGTGCTCTCAAGATGCAGGGGGCAGCCCTGTGGTCACTGCTGAAATGCCTCTTCCCAAGGCTTAC
ATAGAGGAGAACCTAGAGCTGGTTGAAAAAGGCTTCAGTAACTTGAAGAAACAAATTGAAAATGGCAGAATGTTTGGAAT
TCCAGTAGTAGTGGCCGTGAATGCATTCAAGATGGATACAGAGACTGAGCTAGACCTCCTCAGCCACCTTTCCAGAGAAC
ATGGGGCTTTTGATGCCGTGAAGTGCACTCACTGGGCAGAAGGGGGCAAAGGTGCCTTAGCCCTGGCTCAGGCCATCTAG
AGAGCAGCACAAGCACCCAGCAGCTTCCAACTCCTCTATGACCTCAAACTCCCAGTTGAGGATAAAATCAGAATCACTGC
ACAGAAGATCGATGGAGTAGACGACATTGACTTACTCCCCAAAGCTCAACACAAAGCTGAAGTCTACACAAAGCAGGGGT
TTGGGAATCTCCCCATCTGCATGGCCAAAACACATTTGTCCTTGTCTCACAACCCAGAGCAAAAAGGTATTCCTACAGGA
TTTGTTCTGCCCATTTGCGACATCAATGCCAGCATCGGGGCTGGTTTTCTGTACCCTTTAGTAGAAACAGTGAGCACAAT
GGACTCCCCACCCAGCCCTGTTTTTATTGTACTGATTTGGACCCTGAAACAGAACAGGTGAATGGATTATTC

Alignment

ORF - retro_mmul_2583 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.16 %
• Parental protein coverage: 71.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PVPGGVGPMTVAMLMQSTVESAKRFLEKFKPGKWMIEYNNLNLKTPVPSDIDISRSCKLKPIGKLAREIG
          PVPG...PM.VAML.QSTVES.K.FLEKFKPGKWM..YNNLN.KT.VPSDIDISRSCKLKPIGKLAREIG
Retrocopy PVPGSLRPMMVAMLIQSTVESTKCFLEKFKPGKWMNQYNNLNFKTLVPSDIDISRSCKLKPIGKLAREIG

Parental  LLSEEVELYGETKAKVLLSALERLRHRPDGKYVVVTGITPT-PLGEGKSTTTIGLVQALGAHLYQNVFAC
          LLSEEVELYGETKAKVLLSALE.L.H.PDGKY.VVTGITPT...GEGKSTTTIGLVQAL.AH.YQN.F.C
Retrocopy LLSEEVELYGETKAKVLLSALEHLKHQPDGKYRVVTGITPT<TPGEGKSTTTIGLVQALFAHIYQNIFVC

Parental  VRQPSQGP-TFGIKGGAAGGGYSQVIPMEEFNLHLTGDIHAITAANNLVAAAIDARIFHELTQTDKALFN
          ....S.GP..FGIKGGAAGGGYSQ.IPME.FNLHLTGDIHAIT.ANNL.AAAIDA.IFHEL.QTDKALFN
Retrocopy ATAFS-GP>IFGIKGGAAGGGYSQIIPME*FNLHLTGDIHAITVANNLIAAAIDAQIFHELPQTDKALFN

Parental  RLVPSVNGVRKFSDIQIRRLKRLGIEKTDPTTLTDEEINRFARLDIDPETITWQRVLDTNDRFLRKITIG
          RLV.SVNGVRKFSDI.IRRL.RLGIEKTDPTTLTDEEINRF.RLDIDP...TWQRVLDTNDRFLRKI.IG
Retrocopy RLVLSVNGVRKFSDIHIRRLNRLGIEKTDPTTLTDEEINRFVRLDIDPDIKTWQRVLDTNDRFLRKIMIG

Parental  QAPTEKGHTRTAQFDISVASEIMAVLALTTSLEDMRERLGKMVVASSKKGEPVSAEDLGVSGALTVLMKD
          QAPT.KGH.RTAQFDISVASEIMAVLALTTSLEDMRERLGKM.VASSKKGEP..AEDLGV.GAL.VLMKD
Retrocopy QAPTKKGHIRTAQFDISVASEIMAVLALTTSLEDMRERLGKMGVASSKKGEPIRAEDLGVGGALIVLMKD

Parental  AIKPNLMQTLEGTPV-FVHAGPFANIAHGNSSILADR-IALKLVGPEGFVVTEAGFGADIGMEKFFNIKC
          AIKPNLMQTLEGTPV.FVHAGPFANIAHGNS.I.ADR.IALKLVGPEGF.VTE.GFGADIGMEKFFNIK.
Retrocopy AIKPNLMQTLEGTPVPFVHAGPFANIAHGNSPIIADR<IALKLVGPEGFAVTEVGFGADIGMEKFFNIKS

Parental  RYSGLRPHVVVLVATVRALKMH-GGGPTVTAGLPLPKAYIEENLELVEKGFSNLKKQIENARMFGIPVVV
          RYSGL.PHVVVLV.TV.ALKM..GG.P.VTA..PLPKAYIEENLELVEKGFSNLKKQIEN.RMFGIPVVV
Retrocopy RYSGLHPHVVVLVDTVSALKMQ<GGSPVVTAEMPLPKAYIEENLELVEKGFSNLKKQIENGRMFGIPVVV

Parental  AVNAFKTDTEAELDLISRLSREHGAFDAVKCTHWAEGGKGALALAQAVQRAAQAPSSFQLLYDLKLPVED
          AVNAFK.DTE.ELDL.S.LSREHGAFDAVKCTHWAEGGKGALALAQA..RAAQAPSSFQLLYDLKLPVED
Retrocopy AVNAFKMDTETELDLLSHLSREHGAFDAVKCTHWAEGGKGALALAQAI*RAAQAPSSFQLLYDLKLPVED

Parental  KIRIIAQKIYGADDIELLPEAQHKAEVYTKQGFGNLPICMAKTHLSLSHNPEQKGVPTGFVLPIRDIRAS
          KIRI.AQKI.G.DDI.LLP.AQHKAEVYTKQGFGNLPICMAKTHLSLSHNPEQKG.PTGFVLPI.DI.AS
Retrocopy KIRITAQKIDGVDDIDLLPKAQHKAEVYTKQGFGNLPICMAKTHLSLSHNPEQKGIPTGFVLPICDINAS

Parental  VGAGFLYPLVGTMSTMPGLPTRPCF-YDIDLDPETEQVNGLF
          .GAGFLYPLV.T.STM...P..P.F.Y..DLDPETEQVNGLF
Retrocopy IGAGFLYPLVETVSTMDS-PPSPVF<YCTDLDPETEQVNGLF

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	50.42 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	42.68 RPM
SRP007412_cerebellum	0.19 RPM	34.42 RPM
SRP007412_heart	0.00 RPM	38.92 RPM
SRP007412_kidney	0.00 RPM	145.42 RPM
SRP007412_liver	0.04 RPM	538.86 RPM
SRP007412_testis	0.00 RPM	6.75 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2583 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2583 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2583 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015967	1 retrocopy	retro_cfam_300,
Homo sapiens	ENSG00000100714	1 retrocopy	retro_hsap_4839,
Gorilla gorilla	ENSGGOG00000005251	1 retrocopy	retro_ggor_3018,
Microcebus murinus	ENSMICG00000013011	6 retrocopies	retro_mmur_1069, retro_mmur_1250, retro_mmur_1462, retro_mmur_451, retro_mmur_777, retro_mmur_993,
Macaca mulatta	ENSMMUG00000001319	1 retrocopy	retro_mmul_2583 ,
Pan troglodytes	ENSPTRG00000006435	1 retrocopy	retro_ptro_3223,