RetrogeneDB ID: retro_mmul_2617

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:93524693..93525229(-)
• Located in intron of: None

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_2617
CTAGATATTGTCCTCACAGAACTCAGTCCATCAGAGGAATATAAAGCTATGGTATTGGCAGGACTGCAACCAGAGATGGT
GTTGAACATTAGCTCCTGAGCATAATACTTCTGGACATACTATGTATATCAGGAGTCTCTCTATCAAGAATACAATTTCA
GCAAAGCTGAGGGCCATCTGAAACAGATGGAGAAGATATATATTCAGCAAATACAGAGCAAAGATGTAGAATTGACCTTT
ATAAAAGGAGGGATCACCTCCATGAAGAAAGTGCTAAAAGAACACAATAAAAATGTTCACTGATATCTTTTAAAAAATGT
ATGGAGTGCAGTCATAAGTGTCAAAAGCTCCAAAGCCTCTGTGATAGCCTGAGGCTATGAAACATTACTGTTACTAACCA
AGAACATACCTTTGAATCATCCATAATTGCACAGTATGGTGTTTCTGGCTTTTCATTAGGACACAACGCCAAGTGTCTTT
TGGACAGTGCACCAGTTTAAAATCTGGGTGATGGAGATAGAGATTTTCAGTTCAGA

Alignment

ORF - retro_mmul_2617 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70. %
• Parental protein coverage: 64.26 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LDIVRTELSPSEEYKAMVLAGLRPEIVLDISSRALAFWTYQVHQERLYQEYNFSKAEGHLKQMEKIYTQQ
          LDIV.TELSPSEEYKAMVLAGL.PE.VL.ISS.A..FWTY.V.QE.LYQEYNFSKAEGHLKQMEKIY.QQ
Retrocopy LDIVLTELSPSEEYKAMVLAGLQPEMVLNISS*A*YFWTYYVYQESLYQEYNFSKAEGHLKQMEKIYIQQ

Parental  IQSKDVELTSMKGEVTSMKKVLEEYKKK-FSDI-SEKLMERNRQYQKLQGLYDSLRLRNITIANHEGTLE
          IQSKDVELT..KG..TSMKKVL.E..K..F.DI...K.ME.....QKLQ.L.DSLRL.NIT..N.E.T.E
Retrocopy IQSKDVELTFIKGGITSMKKVLKEHNKN>FTDI>FKKCMECSHKCQKLQSLCDSLRL*NITVTNQEHTFE

Parental  PSMIAQSGVLGFPLGNNSRFPLDNTPVRNRGDGDGDFQFK
          .S.IAQ.GV.GF.LG.N....LD..PV.N.GDGD.DFQF.
Retrocopy SSIIAQYGVSGFSLGHNAKCLLDSAPV*NLGDGDRDFQFR

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	0.00 RPM	1.82 RPM
SRP007412_cerebellum	0.00 RPM	12.08 RPM
SRP007412_heart	0.00 RPM	4.12 RPM
SRP007412_kidney	0.00 RPM	8.45 RPM
SRP007412_liver	0.00 RPM	0.40 RPM
SRP007412_testis	0.00 RPM	5.58 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2617 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2617 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2617 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_4197

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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,