RetrogeneDB ID: retro_mmul_457

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:209026270..209027225(+)
• Located in intron of: ENSMMUG00000018891

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLK3
• Ensembl ID: ENSMMUG00000011069
• Aliases: None
• Description: None

Sequence

>retro_mmul_457
GGGAACCTGGGCCAAGGCGCCTGTGGCAAGGGGGTGAGTGCTTGGACCCTGCCAGATGGACGTCTCGGATTGCCCGGGGG
TCATCTGCAATGTGGGCAACTACCGGGAGACGGCACCGCCAAAAATCAACGCTCTCGAAAAAAGTAAACGAGACGGACTA
GGAGAACCAGCTACTGTGTGTCTTGGGGTGTGACTGGTTCACCCTCCACAGTCCGTGTACAGCACTTTAAGCTCCTGGGC
AGGAACACCCTTGAGTTCCCGAAGGAAAATAACTTCCAGCCATTCCCCTCCCACATGTCTGGCACATGGCCCACCAGCTC
TGCACACCCTTAGATTTCTGCATGAGAACCGGCTGACCCACACACGTAAACCAAGAACATCCTGCGTGTGGATTCTGAAT
TACACACCTTCCACAGAGAGCACAGGAGCAATGAGAAGTCAGTGAGGACCACCAGCGTCCGAGTGGCTGACATCCGCAAT
GCCACCGCTGACCGTGAGCATCACACCGCCATGGTGACCACCGTCACTGTCGCCTGCCTGAACTGATCCTTGATCTGGGC
TGGACACGCCCCTGCCATGTCCGGGCCATGGGCTGCATTCTCTTTAAGTACTACCAGGTTTCACACTCTTCCAGACCTAT
GAAAACCAAGAGCACCTGGTGATGATGAAGACCCTAGGGCCCAGCCCATTACGCGTGATCTCCTGTACCAAGAAGCAGAA
ATATTTCTACAAAGAGGGCCTAGTTTGGGATGAGAACAGCTTGGACGGCCCATATGAGAAGAACTGCAAACGTCTGAAGA
GTGACATGCTCCAGGACTCTCTGAAGTACGTGCAGCTGTTTGACCTGATGAGGAGGGTGGTAAAATTGGACCCTGCCCAG
CACATCAAACTGGCTGAGACTCTTCTGCAGCCCTTCTTTGCTGGTCACCCTCAGTCGTGGTCCTTCCAAACCACA

Alignment

ORF - retro_mmul_457 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.28 %
• Parental protein coverage: 51.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  GNLGEGTFGKVV-ECLDHARGKFQVALK-IIRNVGKYREAARLEINVL-KKIKEKDKENKFLCVLMSDWF
          GNLG.G..GK.V.ECLD.AR.....A....I.NVG.YRE.A...IN.L.KK..E.D.EN..LCVL..DWF
Retrocopy GNLGQGACGKGV<ECLDPARWTSRIARG<VICNVGNYRETAPPKINAL>KKVNETD*ENQLLCVLGCDWF

Parental  NFHGHMCIA-FELLGKNTFEFLKENNFQPYP-LPHVRHMAYQLC-HALRFLHENQLTHTDLKP-ENILFV
          ..H...C.A.F.LLG.NT.EF.KENNFQP.P.LPHV.HMA.QLC.H.LRFLHEN.LTHT..KP..NIL.V
Retrocopy TLHSP-CTA>FKLLGRNTLEFPKENNFQPFP<LPHVWHMAHQLC<HTLRFLHENRLTHTR-KP<KNILRV

Parental  NSEFETLYNEHKSCEEKSVKNTSIRVADFGSATFDHEHHTTIVAT-RHYRPPEVILELGWAQPCDVWSIG
          .SE..T...EH.S..EKSV..TS.RVAD...AT.D.EHHT..V.T.RH.R.PE.IL.LGW..PC.V...G
Retrocopy DSELHTFHREHRS-NEKSVRTTSVRVADIRNATADREHHTAMVTT<RHCRLPELILDLGWTRPCHVRAMG

Parental  CILFEYYR-GFTLFQTHENREHLVMMEKILGPIPSHMIHRTRKQKYFYKGGLVWDENSSDGRYVKENCKP
          CILF.YY..GFTLFQT.EN.EHLVMM.K.LGP.P...I..T.KQKYFYK.GLVWDENS.DG.Y.K.NCK.
Retrocopy CILFKYYQ<GFTLFQTYENQEHLVMM-KTLGPSPLRVISCTKKQKYFYKEGLVWDENSLDGPYEK-NCKR

Parental  LKSYMLQDSLEHVQLFDLMRRMLEFDPAQRITLAEALLHPFFAGLTPEERSFHTS
          LKS.MLQDSL..VQLFDLMRR....DPAQ.I.LAE.LL.PFFAG..P...SF.T.
Retrocopy LKSDMLQDSLKYVQLFDLMRRVVKLDPAQHIKLAETLLQPFFAG-HPQSWSFQTT

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	23.53 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	24.83 RPM
SRP007412_cerebellum	0.00 RPM	28.74 RPM
SRP007412_heart	0.00 RPM	16.08 RPM
SRP007412_kidney	0.00 RPM	23.00 RPM
SRP007412_liver	0.00 RPM	21.73 RPM
SRP007412_testis	0.15 RPM	86.32 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_457 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_457 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_457 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000179335	1 retrocopy	retro_hsap_540,
Macaca mulatta	ENSMMUG00000011069	1 retrocopy	retro_mmul_457 ,
Macaca mulatta	ENSMMUG00000023141	1 retrocopy	retro_mmul_1627,
Pan troglodytes	ENSPTRG00000007278	1 retrocopy	retro_ptro_405,