RetrogeneDB ID: retro_mmul_612

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 10:64542837..64544066(+)
• Located in intron of: ENSMMUG00000008152

Retrocopy information

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

Parental gene information

• Parental gene symbol: KLHL12
• Ensembl ID: ENSMMUG00000017849
• Aliases: None
• Description: kelch-like protein 12 [Source:RefSeq peptide;Acc:NP_001253268]

Sequence

>retro_mmul_612
AGCCAGAAGCATTTTCCTGAAGTGGTGTAGCATGAAGAGTTCATTCTTCTGAGTCAAGGAGGGGTGGAAAAGCTAATCAA
GTGCGATGAAATTCAGGTGGATTCTGAAGAGCCAGTCTTTGAGGCTGTCATCAACTGCCTGAAGCACGTCAAGAAACAGC
GGGAAAAACCCTTGCCTAACCTGCTACAGTATGTGCGGATGCCCCTGCTAACCCCCAGGTATATCACAGATGTAACAGAT
GCTGAGCCTTTCTTCCGCTGTAGTTTACAATGCAGGGATCTGGTGGATGAAGCAAAGAAGTTTCATCTGAGGCCTGAACT
TCAGTGTCAGATGCAGGGACCCAGGACAAGGGCTCACCTAGGAGCCAATGAAGTGCTTTTGGTGGCTGGGGGCTTCGGAA
GCCAGCAGTCTCCCACTGACGTGGTAGAGAAATACGACCCTAAGACTCAGGAGTGGAGATTTTTGCCAAACATCACTCGT
AACAGACATTATGTGGCCTCAGTGTCCCTACATGACCGAATCTACATTATTGGTGGCTATGATAGCTGTTCCTGCCTTAG
TTCAGTGGAATGTCTAGACTACATAGCAGATGAGGATGGGGTCTGGTATTCTGTGACCCCGATTAATGTCTGACAAGGTC
TTGCTGGAGCCACCACCCGGGGAGATATGATCTGTGTCTCTGGAGACTTTGATGGAAGCAGGTGTCACACCAGTATGGAG
TGGTATGATCCAAACATTGACCAGTGGAGCATGCTGGGAGATATGCAGGCAGCCCAGGAAGGTGCTGGACCCGTAGTGGC
CAGTGGAGTGATCCACTGTCTAGGAGGGTATGACGGCTTGAATATCTTAAATTCAGTTGAGAAATATACCCTCATACAGG
ACATCGGACTAATGTTACATCAATGGCCATCGAGTGTTCTGGTGTGGGAGTAGCCCTGCTGAATGACCATATTTATGTGG
TGGGGGGATTTGATGGTACAGCCCACCTTTCTTCCAATGAAGCATACAACATTCTCACTGATTCCTGGACAACTGTCACC
AATATGACCACTCTACGATGCAATGTAGGGGCCACAGTGCTTTGGGGGAGACTCTATGCAACTTCAGGATATGATGGTAA
TTCCCTGCTAAGTAGCATTGAATGTTATGACCCTATCATCAACAGCTGGGAAGTCGTGACATCCATGGGAACCCAGTGCT
GTGATGCTGGTGTGTGTTCTCCACAAGAA

Alignment

ORF - retro_mmul_612 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.89 %
• Parental protein coverage: 72.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SQKHFPEVVQHEEFILLSQGEVEKLIKCDEIQVDSEEPVFEAVINWVKHAKKEREESLPNLLQYVRMPLL
          SQKHFPEVV.HEEFILLSQG.VEKLIKCDEIQVDSEEPVFEAVIN..KH.KK.RE..LPNLLQYVRMPLL
Retrocopy SQKHFPEVV*HEEFILLSQGGVEKLIKCDEIQVDSEEPVFEAVINCLKHVKKQREKPLPNLLQYVRMPLL

Parental  TPRYITDVIDAEPFIRCSLQCRDLVDEAKKFHLRPELRSQMQGPRTRARLGANEVLLVVGGFGSQQSPID
          TPRYITDV.DAEPF.RCSLQCRDLVDEAKKFHLRPEL..QMQGPRTRA.LGANEVLLV.GGFGSQQSP.D
Retrocopy TPRYITDVTDAEPFFRCSLQCRDLVDEAKKFHLRPELQCQMQGPRTRAHLGANEVLLVAGGFGSQQSPTD

Parental  VVEKYDPKTQEWSFLPSITRKRRYVASVSLHDRIYVIGGYDGRSRLSSVECLDYTADEDGVWYSVAPMNV
          VVEKYDPKTQEW.FLP.ITR.R.YVASVSLHDRIY.IGGYD..S.LSSVECLDY.ADEDGVWYSV.P.NV
Retrocopy VVEKYDPKTQEWRFLPNITRNRHYVASVSLHDRIYIIGGYDSCSCLSSVECLDYIADEDGVWYSVTPINV

Parental  RRGLAGATTLGDMIYVSGGFDGSRRHTSMERYDPNIDQWSMLGDMQTAREGAGLVVASGVIYCLGGYDGL
          ..GLAGATT.GDMI.VSG.FDGSR.HTSME.YDPNIDQWSMLGDMQ.A.EGAG.VVASGVI.CLGGYDGL
Retrocopy *QGLAGATTRGDMICVSGDFDGSRCHTSMEWYDPNIDQWSMLGDMQAAQEGAGPVVASGVIHCLGGYDGL

Parental  NILNSVEKYD-PHTGHWTNVTPMATKRSGAGVALLNDHIYVVGGFDGTAHLSSVEAYNIRTDSWTTVTSM
          NILNSVEKY..PHTGH.TNVT.MA...SG.GVALLNDHIYVVGGFDGTAHLSS.EAYNI.TDSWTTVT.M
Retrocopy NILNSVEKYT<PHTGHRTNVTSMAIECSGVGVALLNDHIYVVGGFDGTAHLSSNEAYNILTDSWTTVTNM

Parental  TTPRCYVGATVLRGRLYAIAGYDGNSLLSSIECYDPIIDSWEVVTSMGTQRCDAGVCVLRE
          TT.RC.VGATVL.GRLYA..GYDGNSLLSSIECYDPII.SWEVVTSMGTQ.CDAGVC...E
Retrocopy TTLRCNVGATVLWGRLYATSGYDGNSLLSSIECYDPIINSWEVVTSMGTQCCDAGVCSPQE

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	2.58 RPM	50.87 RPM
SRP007412_brain_prefrontal_cortex	1.67 RPM	43.39 RPM
SRP007412_cerebellum	4.00 RPM	44.30 RPM
SRP007412_heart	0.82 RPM	19.84 RPM
SRP007412_kidney	1.17 RPM	52.35 RPM
SRP007412_liver	1.03 RPM	19.63 RPM
SRP007412_testis	1.02 RPM	87.60 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_612 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_612 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_612 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006231	1 retrocopy	retro_cjac_2151,
Dasypus novemcinctus	ENSDNOG00000010436	1 retrocopy	retro_dnov_2190,
Echinops telfairi	ENSETEG00000007800	2 retrocopies	retro_etel_2103, retro_etel_723,
Homo sapiens	ENSG00000117153	1 retrocopy	retro_hsap_2545,
Macaca mulatta	ENSMMUG00000017849	1 retrocopy	retro_mmul_612 ,
Nomascus leucogenys	ENSNLEG00000018103	1 retrocopy	retro_nleu_2795,
Otolemur garnettii	ENSOGAG00000014771	1 retrocopy	retro_ogar_1552,
Pongo abelii	ENSPPYG00000000343	1 retrocopy	retro_pabe_1872,
Pan troglodytes	ENSPTRG00000001861	1 retrocopy	retro_ptro_1483,