RetrogeneDB ID: retro_mmul_2285

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:30255823..30256640(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4375
• Ensembl ID: ENSMMUG00000016840
• Aliases: None
• Description: dual specificity mitogen-activated protein kinase kinase 1 [Source:RefSeq peptide;Acc:NP_001244478]

Sequence

>retro_mmul_2285
TGCATGAGTGCAACTCTCGTGGGCTTCTGTGGTGCATTCTACAGTGAGAGGCGAGATCAGTATCTGCATGTAGCACATGG
ATGGAGGTTCCCTGGATCAAGTCCTGAAGAAAGCTGGAAGAATTCCTGAACAAATTTTAGAAAAAGTTAGCGTTGCTGTA
ATAAAAGGCCTGACATATCTGAGGGAGAAGCACAAGATCATGCACAGAGATGTCCAGCCCTCCCACATCCTAGTCAAGTC
CCGTGGGGAAATCAAGCTCTGTAACTTTGGGGTCAGTGGGCAGCTCATCAACTCCATGGCCAACTCCTTCGTGGGCCCAA
AGTCCTACATGTCACCAGAAAGATTCCAGGGGACTCATTACTCTGTGCAGTCAGACATCTGGAACATGGGATTTTCTCTG
GTAGAGATGGCAGTTGGGAGGTATCCCATCCCTCCTCCAGATGGCAAGGAGCTGGAGCTGATGTTTGGGTGCCAGGTGGA
GGGAGATGCGGCTGAGACCCCACCCAGGCCAAGGACCCCAGGGAGGCCCCTTAGCTCATAAGGAATGGACAGCCGACCTC
CCATGGCAATTTTTGAGTTGTTGGATTACCTAATCAACGAGCCTCCTCCAAAAATGCCCAGAGTGTTCACTTTGGAATTT
CAAGATTTTGTGAATAAATGCCTAATTTAAAACCCCGCAGAGAGAGCAGATTTGAAGAAACTCATGGTTCATGCTTTTCT
CAAGAGATCTGATGCTGAAGAAGTGGATTTTGCAGGTTGGCTCTGCTCCACTGTCGGCCTTAACCAGCCCAGCATGCCAA
CCCATGCTACTGGCATG

Alignment

ORF - retro_mmul_2285 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.86 %
• Parental protein coverage: 69.47 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CNSPYIVGFYGAFYSD-GEISICMEHMDGGSLDQVLKKAGRIPEQILGKVSIAVIKGLTYLREKHKIMHR
          C.S...VGF.GAFYS..GEISICM.HMDGGSLDQVLKKAGRIPEQIL.KVS.AVIKGLTYLREKHKIMHR
Retrocopy CMSATLVGFCGAFYSE>GEISICM*HMDGGSLDQVLKKAGRIPEQILEKVSVAVIKGLTYLREKHKIMHR

Parental  DVKPSNILVNSRGEIKLCDFGVSGQLIDSMANSFVGTRSYMSPERLQGTHYSVQSDIWSMGLSLVEMAVG
          DV.PS.ILV.SRGEIKLC.FGVSGQLI.SMANSFVG..SYMSPER.QGTHYSVQSDIW.MG.SLVEMAVG
Retrocopy DVQPSHILVKSRGEIKLCNFGVSGQLINSMANSFVGPKSYMSPERFQGTHYSVQSDIWNMGFSLVEMAVG

Parental  RYPIPPPDAKELELMFGCQVEGDAAETPPRPRTPGRPLSSYGMDSRPPMAIFELLDYIVNEPPPKLPSGV
          RYPIPPPD.KELELMFGCQVEGDAAETPPRPRTPGRPLSS.GMDSRPPMAIFELLDY..NEPPPK.P..V
Retrocopy RYPIPPPDGKELELMFGCQVEGDAAETPPRPRTPGRPLSS*GMDSRPPMAIFELLDYLINEPPPKMPR-V

Parental  FSLEFQDFVNKCLIKNPAERADLKQLMVHAFIKRSDAEEVDFAGWLCSTIGLHQPSTPTHAAGV
          F.LEFQDFVNKCLI.NPAERADLK.LMVHAF.KRSDAEEVDFAGWLCST.GL.QPS.PTHA.G.
Retrocopy FTLEFQDFVNKCLI*NPAERADLKKLMVHAFLKRSDAEEVDFAGWLCSTVGLNQPSMPTHATGM

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	1.79 RPM	191.38 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	193.41 RPM
SRP007412_cerebellum	0.71 RPM	75.75 RPM
SRP007412_heart	0.29 RPM	35.21 RPM
SRP007412_kidney	0.47 RPM	43.66 RPM
SRP007412_liver	0.08 RPM	24.78 RPM
SRP007412_testis	0.08 RPM	16.21 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2285 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2285 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2285 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2676
Gorilla gorilla	retro_ggor_2650
Pongo abelii	retro_pabe_3249

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033983	1 retrocopy	retro_btau_1416,
Cavia porcellus	ENSCPOG00000003053	1 retrocopy	retro_cpor_483,
Gorilla gorilla	ENSGGOG00000003687	1 retrocopy	retro_ggor_2650,
Macaca mulatta	ENSMMUG00000016840	1 retrocopy	retro_mmul_2285 ,
Otolemur garnettii	ENSOGAG00000015876	1 retrocopy	retro_ogar_1598,
Ochotona princeps	ENSOPRG00000007770	1 retrocopy	retro_opri_846,
Pongo abelii	ENSPPYG00000006576	2 retrocopies	retro_pabe_3092, retro_pabe_3249,
Pan troglodytes	ENSPTRG00000007193	1 retrocopy	retro_ptro_2676,