RetrogeneDB ID: retro_mmul_1455

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:107550402..107551925(+)
• Located in intron of: ENSMMUG00000005187

Retrocopy information

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

Parental gene information

• Parental gene symbol: LRRFIP1
• Ensembl ID: ENSMMUG00000003386
• Aliases: LRRFIP1, LRRFIP2
• Description: None

Sequence

>retro_mmul_1455
ATGACCAGCCCCGCAGCCGCGCAGAGCCAGGAGATCGACTGTTTGAGACCGGAAGGGCAGAGGCTGGCGGAGGCCCCGCT
CGCGGCAACACTGGCGGCCGGGGCGGAGGCTCGTGAGATCCGCATGAAGGAGCTGGAGCGGCAGCAGAAGGAGGTAGAAG
AGGGACCAGAAAAAGATTTTACTGAGAAGGGGTCTGGTAACACGCCAGGCCTGTCTGCAGCCACGCTGGCCTCTCTGGTT
GGGAGTTGCTCTCAGAGAGGCAGCTGGAGACACCTCCATCTCCATCCACACTAAGGCCTCCATCAGGGAAATAAAGAACT
CTCTAGCAGAAGTTGAAGAGAAATATAAGAAGGCTATGGTTTCCAATGCTCAGCTATACAATGAAAAGACAAACTTCATG
TACCGGGTTGATACCTTGAAAGATACGTTGCTGGAGCTTGAAGAACAGCTGACTGAATCTAGGCAGCAGTACAAAGAGAA
AAAGAATTTGAAAGGGAAAAACATGCCCACAGTATACTGCAATTTCAGTTTGCTGAAGTCAAGGAGGCCCTGAAGCAAAG
AGAGGAAATGCTCGAGAAACATGGAATAATCCTAAATTCAGAAATAGCTACCAATGGAGAGACTTCCGACACTCTCAATA
ATGTTGGATACCAAGGTCCTACCAAGATGACGAAAGAAGGGTTAAATGCCCTCAAGTCGACAGGGGATGGGACCCTAGGA
AGAGCCAGTGAAGTGGAGGTGAAAAATGAAATCGTGGCGAATGTGGGGAAAAGAGAAATCTTGAACAATACTGAGAAAGA
ATAACACACAGAGGACATAGTGAAGGACTGTGTGGATATAGAGGTATTCCCTGCTGGTGAGAATACCGAGGACCAGAAAT
CTTCTGAAGACACTGCCCCATTCCTAGGAACCTTAGCAGGAGCTACCTATGAGGAAGAGGTTCAAAGCCAAATTCTTGAG
AGCGTTTCTCTCCCTGAAAACACAGCACAGGTTGAGTCAAATGAGGTCATGGGTGCACCAGATGACGGGACCAGAACTCC
CCTTGAGCCATCGAACTGTTGGAGTGACTTAGATGGTGGGAGCCACATAGAGAATGTGGGAAAGTCAACGGTGACTCAGG
TTGGAGAGCAGGCAGGCACAGTGGCCTCGTGCCCTTTAAAGCATAGTGATGACACAGTTTATCATGATGACAGATGTACG
GTAGAGGTCCCCCAGAGTTAGAGACAAGCACAGGGCATAGTTTAGATAAAGAATTCACCAACCAGGAAGTAGCGGAGCCC
AAGGAGTTTCCAGTGCATAGTACAGAAGTAGGTAGGGATCACAACGAAGAAGAGGGTAAAGAAACAGGATTAAGGGATGA
GAAACCAATCAAGACAGAAGTTCCTGGCTCTCCAGCAGGAACTGAGAGCAATGGTCAGGAAGCGACAGGTCCAAGTACAG
TAGACACTCAAAGTAAACCCTTAGATATGAAAGAGTCTGACGAAGAAAAGACTGACCAAAAGGGAGACGCATTGGACTCA
TCG

Alignment

ORF - retro_mmul_1455 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.55 %
• Parental protein coverage: 67.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MTSPAAAQSREIDCLSPEAQRLAEARLAAKRAARAEAREIRMKELERQQKEVEDRPEKDFTEKGSRNMPG
          MTSPAAAQS.EIDCL.PE.QRLAEA.LAA..AA.AEAREIRMKELERQQKEVE..PEKDFTEKGS.N.PG
Retrocopy MTSPAAAQSQEIDCLRPEGQRLAEAPLAATLAAGAEAREIRMKELERQQKEVEEGPEKDFTEKGSGNTPG

Parental  LSAATLASLGGTSSRRGS-GDTSISIDTEASIREIKDSLAEVEEKYKKAMVSNAQLDNEKTNFMYQVDTL
          LSAATLASL.G..S.RGS.GDTSISI.T.ASIREIK.SLAEVEEKYKKAMVSNAQL.NEKTNFMY.VDTL
Retrocopy LSAATLASLVGSCSQRGS>GDTSISIHTKASIREIKNSLAEVEEKYKKAMVSNAQLYNEKTNFMYRVDTL

Parental  KDMLLELEEQLAESRRQYE-EKNKEFEREKHAHSILQFQFAEVKEALKEREEMLEKHGIILNSEIATNGE
          KD.LLEL.E......RQ......KEFEREKHAHSILQFQFAEVKEALK.REEMLEKHGIILNSEIATNGE
Retrocopy KDTLLEL-EEQLTESRQQY<QREKEFEREKHAHSILQFQFAEVKEALKQREEMLEKHGIILNSEIATNGE

Parental  TSDTLNNVGYQGPTKMTKAELNALKSTGDGTLGRASEVEVKNEIVANVGKREILHNTEKEQHTEDTVKDC
          TSDTLNNVGYQGPTKMTK..LNALKSTGDGTLGRASEVEVKNEIVANVGKREIL.NTEKE.HTED.VKDC
Retrocopy TSDTLNNVGYQGPTKMTKEGLNALKSTGDGTLGRASEVEVKNEIVANVGKREILNNTEKE*HTEDIVKDC

Parental  VDIEVFPAGENTEDQKSSEDTAPFLGTLAGATYEEQVQNQILESTSLPENTAQAESDEVMGVPDDRTRTP
          VDIEVFPAGENTEDQKSSEDTAPFLGTLAGATYEE.VQ.QILES.SLPENTAQ.ES.EVMG.PDD.TRTP
Retrocopy VDIEVFPAGENTEDQKSSEDTAPFLGTLAGATYEEEVQSQILESVSLPENTAQVESNEVMGAPDDGTRTP

Parental  LEPSSCWNDLDGGNHTGNVGEAAATQVGEQAGTVASCPLGHSDDTVYHDDKCTVEVPQ-ELETSTGHSLE
          LEPS.CW.DLDGG.H..NVG....TQVGEQAGTVASCPL.HSDDTVYHDD.CTVEVPQ.ELETSTGHSL.
Retrocopy LEPSNCWSDLDGGSHIENVGKSTVTQVGEQAGTVASCPLKHSDDTVYHDDRCTVEVPQ<ELETSTGHSLD

Parental  KEFTNQEAAEPKEVPVQSTEVGRDHNEEEGEETVLRDEKPIKTEVPGSPAGTENNGQEATGPSTVDTQSE
          KEFTNQE.AEPKE.PV.STEVGRDHNEEEG.ET.LRDEKPIKTEVPGSPAGTE.NGQEATGPSTVDTQS.
Retrocopy KEFTNQEVAEPKEFPVHSTEVGRDHNEEEGKETGLRDEKPIKTEVPGSPAGTESNGQEATGPSTVDTQSK

Parental  SLDMKEPEEEKNDQQGEALDSS
          .LDMKE..EEK.DQ.G.ALDSS
Retrocopy PLDMKESDEEKTDQKGDALDSS

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	2.69 RPM	80.23 RPM
SRP007412_brain_prefrontal_cortex	0.71 RPM	52.91 RPM
SRP007412_cerebellum	2.45 RPM	10.27 RPM
SRP007412_heart	2.30 RPM	113.71 RPM
SRP007412_kidney	3.87 RPM	46.71 RPM
SRP007412_liver	0.59 RPM	25.61 RPM
SRP007412_testis	2.07 RPM	5.88 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1455 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1455 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1455 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2887
Gorilla gorilla	retro_ggor_2001

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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	ENSG00000124831	1 retrocopy	retro_hsap_2887,
Gorilla gorilla	ENSGGOG00000008411	1 retrocopy	retro_ggor_2001,
Macaca mulatta	ENSMMUG00000003386	1 retrocopy	retro_mmul_1455 ,
Macaca mulatta	ENSMMUG00000022539	1 retrocopy	retro_mmul_2595,