RetrogeneDB ID: retro_mmul_371

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:47884489..47885243(+)
• Located in intron of: ENSMMUG00000005342

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNB1IP1
• Ensembl ID: ENSMMUG00000016251
• Aliases: None
• Description: None

Sequence

>retro_mmul_371
TCTGGCTATGCATGGGTCACTGCCTGCTCTCACGTCTTCTGTGATCAGCATGGCAGTGGTGAGTTAAGTTGCTCACCAGC
TATCTGTGATGCCTGAAAAGTACCCTTTCTGGAAAGCTAGATATTGTCCACACAGAACTCAGTCCATCAGAGAAATATAA
AGCTATGGTATTGGCAGGACTGCGACAAGAGATCGTGTAGGACATTAACTCCCGAGCAGTGGCCTTCAGGACATATCAGG
TACATCAGGAACGTCTCTATCAAGAACACAATTTCATCAAGGCTGAGGGCCATCTGAAACAAATGGATAAGATATATACT
CAGCAAATACAAAGCAAGGATGTAGAATTGATCTCTATGAAAGGGGAGGTCACCTCCATGAAGAAAGTGCTAGAAGAATA
CAAGAAAAAGTTCAGTGACATCTCTGAGAAACTTAAGGAACGCAATCTTCAGTATCAAAAGCTCCAAGGCCTCTATGATA
GCCTTAGGCTATGTAACATCCCTATTGCTAACCATGAAGGCACCTTGAACCATCTGTGATTGCACAGTCTGGTGTTTTTG
GCTTCCCATTAGGAATAACAACCCCAAGTTTCCTTTGGATAGTACACCTGTTTGAAATCGGGGCGATGGAGATTTTCAGT
TCAGACCATTTTTTTGTAGGCTCTCCCATAGCACCTGAACCCAGCAACAGCTTATTTAGTTTTGCCTCTCCAAGGGGCGA
ATTAGAGCAGCAGCAAGTTTCTAGCAGGGCCTTC

Alignment

ORF - retro_mmul_371 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.88 %
• Parental protein coverage: 91.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SGYAWVTACSHIFCDQHGSGEFSRSPAICPA-CNSTLSGKLDIVRTELSPSEEYKAMVLAGLRPEIVLDI
          SGYAWVTACSH.FCDQHGSGE.S.SPAIC.A...STLSGKLDIV.TELSPSE.YKAMVLAGLR.EIV.DI
Retrocopy SGYAWVTACSHVFCDQHGSGELSCSPAICDA<LKSTLSGKLDIVHTELSPSEKYKAMVLAGLRQEIV*DI

Parental  SSRALAFWTYQVHQERLYQEYNFSKAEGHLKQMEKIYTQQIQSKDVELTSMKGEVTSMKKVLEEYKKKFS
          .SRA.AF.TYQVHQERLYQE.NF.KAEGHLKQM.KIYTQQIQSKDVEL.SMKGEVTSMKKVLEEYKKKFS
Retrocopy NSRAVAFRTYQVHQERLYQEHNFIKAEGHLKQMDKIYTQQIQSKDVELISMKGEVTSMKKVLEEYKKKFS

Parental  DISEKLMERNRQYQKLQGLYDSLRLRNITIANHEGT-LEPSMIAQSGVLGFPLG-NNS-RFPLDNTPVRN
          DISEKL.ERN.QYQKLQGLYDSLRL.NI.IANHEGT.LEPS.IAQSGV.GFPLG.NN...FPLD.TPV.N
Retrocopy DISEKLKERNLQYQKLQGLYDSLRLCNIPIANHEGT<LEPSVIAQSGVFGFPLG<NNNPKFPLDSTPV*N

Parental  RGDGDGDFQFKP-FFVGSPTAPEPSNSFFSFASPSRELEQQQVSSRAF
          R..GDGDFQF.P.FFVGSP.APEPSNS.FSFASP..ELEQQQVSSRAF
Retrocopy R--GDGDFQFRP>FFVGSPIAPEPSNSLFSFASPRGELEQQQVSSRAF

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	3.92 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	1.82 RPM
SRP007412_cerebellum	0.06 RPM	12.08 RPM
SRP007412_heart	0.00 RPM	4.12 RPM
SRP007412_kidney	0.12 RPM	8.45 RPM
SRP007412_liver	0.04 RPM	0.40 RPM
SRP007412_testis	0.08 RPM	5.58 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_371 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_371 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_371 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009967	2 retrocopies	retro_cjac_3244, retro_cjac_4197,
Homo sapiens	ENSG00000100814	1 retrocopy	retro_hsap_4877,
Gorilla gorilla	ENSGGOG00000004586	1 retrocopy	retro_ggor_3046,
Microcebus murinus	ENSMICG00000000893	2 retrocopies	retro_mmur_1264, retro_mmur_1551,
Macaca mulatta	ENSMMUG00000016251	2 retrocopies	retro_mmul_2617, retro_mmul_371 ,
Nomascus leucogenys	ENSNLEG00000010636	1 retrocopy	retro_nleu_2556,
Pan troglodytes	ENSPTRG00000006088	1 retrocopy	retro_ptro_3249,
Rattus norvegicus	ENSRNOG00000026056	1 retrocopy	retro_rnor_842,
Ictidomys tridecemlineatus	ENSSTOG00000004394	1 retrocopy	retro_itri_1590,