RetrogeneDB ID: retro_mmul_879

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:72282508..72283085(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNG2
• Ensembl ID: ENSMMUG00000000914
• Aliases: None
• Description: None

Sequence

>retro_mmul_879
GATCTAAGAGATTTAACTAACTTTTTTTGAATCTTCTCCAGAAACTTTTATTGTGGCTGCCAATATTTTGGACAGGTCCT
TGGCTTTTCTGAAGGTAGAACCTAAAATTCATCTTTCACTGGAGTCTATTGTTTATGCTGGTTACCAGAATAGTTGAAAA
AGAATGCAATGTTTTATCTACTCATGAAGTAATCTTGATTCGTCAATGTAAATGCACTGCTTCTTCTGACAGAAAACTAA
TGGAAAAATAATTTCAAAAAAAATCAGAACTATGAATTGGAACCTACTGTACCTTAAACTTCTTTTGCTTCTGTAAGACT
ATCATATTTCTTTATATTTGAAAAAGGAAAGAAATATTGGATCTTATAAACTGGAAGCTCAACTGAAAACTTTCAATCTT
TTGCTAATCTTTTCAAAAGCAAAACCATCTGTATTAGTTTTGCGTCTTCTTAATCTGGAAGTAGAAATGTAATTTAGTGA
GTTATTGAAAAATTTCCTGCTTCTTATAAGGCATTCAAAGATTAATGAAACCGAATTCTTTTAGTGGAGGGAAGTAGTTT
CTAAATGGCTAGCTGAA

Alignment

ORF - retro_mmul_879 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.51 %
• Parental protein coverage: 56.43 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DLRSLANFFGSCTETFVLAVNILDRFLALMKVKPKHLSCIGVCS-FLLAARIVEEDCNIPSTHDVIRISQ
          DLR.L.NFF......F..........L..........S..GV...F.L..RIVE..CN..STH.VI.I.Q
Retrocopy DLRDLTNFF*IFSRNFYCGCQYFGQVLGFSEGRT*NSSFTGVYC<FMLVTRIVEKECNVLSTHEVILIRQ

Parental  CKCTAS-DIKRMEKIISEKLHYELEATTALNFLHLYHTIILCHTSERKEILSL-DKLEAQLKACNCRLVF
          CKCTAS.D.K.MEK...............LNF.....TII......RKEIL.L..KLEAQLK..N..L.F
Retrocopy CKCTASSDRKLMEK*FXXXSEL*IGTYCTLNFFCFCKTIIFLYI*KRKEILDL<YKLEAQLKTFNLLLIF

Parental  SKAKPSVLALCLLNLEVETLKSVELLEILLLVKKHSKINDAEFFYWRELVSKCLAE
          SKAKPSVL.L.LLNLEVE...S.ELL...LL...HSKIN..EFF.WRE.VSK.LAE
Retrocopy SKAKPSVLVLRLLNLEVEM*FS-ELLKNFLLLIRHSKINETEFF*WREVVSKWLAE

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	20.84 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	13.88 RPM
SRP007412_cerebellum	0.00 RPM	44.88 RPM
SRP007412_heart	0.00 RPM	5.77 RPM
SRP007412_kidney	0.00 RPM	14.67 RPM
SRP007412_liver	0.00 RPM	5.23 RPM
SRP007412_testis	0.00 RPM	4.86 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_879 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_879 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_879 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_773
Sus scrofa	retro_sscr_813

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013793	1 retrocopy	retro_amel_960,
Dasypus novemcinctus	ENSDNOG00000005210	1 retrocopy	retro_dnov_2498,
Felis catus	ENSFCAG00000026008	1 retrocopy	retro_fcat_1062,
Macropus eugenii	ENSMEUG00000008707	1 retrocopy	retro_meug_1962,
Macaca mulatta	ENSMMUG00000000914	1 retrocopy	retro_mmul_879 ,
Macaca mulatta	ENSMMUG00000019904	1 retrocopy	retro_mmul_2529,
Monodelphis domestica	ENSMODG00000011779	1 retrocopy	retro_mdom_358,
Nomascus leucogenys	ENSNLEG00000008169	1 retrocopy	retro_nleu_933,
Pongo abelii	ENSPPYG00000014867	1 retrocopy	retro_pabe_942,
Pan troglodytes	ENSPTRG00000016196	1 retrocopy	retro_ptro_773,
Sus scrofa	ENSSSCG00000008988	1 retrocopy	retro_sscr_813,
Ictidomys tridecemlineatus	ENSSTOG00000027922	1 retrocopy	retro_itri_1112,
Tupaia belangeri	ENSTBEG00000007671	2 retrocopies	retro_tbel_2258, retro_tbel_38,
Tursiops truncatus	ENSTTRG00000014837	1 retrocopy	retro_ttru_491,