RetrogeneDB ID: retro_mmul_794

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:17222070..17222628(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNPS1
• Ensembl ID: ENSMMUG00000019238
• Aliases: None
• Description: RNA binding protein S1, serine-rich domain [Source:HGNC Symbol;Acc:10080]

Sequence

>retro_mmul_794
AGCTCTTCCGGCTCTCCAAGTCCTTCTCGGCGCAGACAAGACAACGGGAGGCGCTCCCGCTCCAAAACCAAACCACCTGA
AAGAGATGAAAAGGAGAGGAAAAGGCGGAGCCCATCTCCTAAGCCCACCAAAGTGCATATTGGGAGACTCACCAGGAATG
TGACAAAGGATCACATCATGGAGATATTTTCCACCTATGGGAAAATTAAAATGATTGACATGCCCGTGGAAAGGATGCAT
CCCCATCTGTCCAAAGGCTGTGCATACGTAGAGTTTGAGAATCCAGATGAAGCTGACAAGGCGCTGAAGCACATGGATGG
AGGACAAATCGATGGTCAGGAGATCACTGCCACTGCCGTGCTGGCCCCCTGGCCTAGGCCACCCCTCAGGAGATTCAGCC
CTCCCAGGAGAATGTTGCCACCACCGCCCACGTGGCGCAGGTCTCCCCCACGGATGAGGAGAAAGTCCCGCTCCCCTAGG
CGCAGGTCCCGCGTGCGCCGGAGATGATGCTCCCCGGGCCGCCGCCGCCACAGGAGCCGCTCCAGTTCCAACTCCTCC

Alignment

ORF - retro_mmul_794 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.55 %
• Parental protein coverage: 65.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSSGSPSPSRRRHDNRRRSRSKSKPPKRDEKERKRRSPSPKPTKVHIGRLTRNVTKDHIMEIFSTYGKIK
          SSSGSPSPSRRR.DN.RRSRSK.KPP.RDEKERKRRSPSPKPTKVHIGRLTRNVTKDHIMEIFSTYGKIK
Retrocopy SSSGSPSPSRRRQDNGRRSRSKTKPPERDEKERKRRSPSPKPTKVHIGRLTRNVTKDHIMEIFSTYGKIK

Parental  MIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAPWPRPPPRRFSPPRRMLP
          MIDMPVERMHPHLSKG.AYVEFENPDEA.KALKHMDGGQIDGQEITATAVLAPWPRPP.RRFSPPRRMLP
Retrocopy MIDMPVERMHPHLSKGCAYVEFENPDEADKALKHMDGGQIDGQEITATAVLAPWPRPPLRRFSPPRRMLP

Parental  PPPMWRRSPPRMRRRSRSPRRRSPVRRRSRSPGRRRHRSRSSSNSS
          PPP.WRRSPPRMRR.SRSPRRRS.VRRR..SPGRRRHRSRSSSNSS
Retrocopy PPPTWRRSPPRMRRKSRSPRRRSRVRRR*CSPGRRRHRSRSSSNSS

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	70.26 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	115.27 RPM
SRP007412_cerebellum	0.06 RPM	68.19 RPM
SRP007412_heart	0.00 RPM	44.16 RPM
SRP007412_kidney	0.00 RPM	52.82 RPM
SRP007412_liver	0.00 RPM	30.64 RPM
SRP007412_testis	0.04 RPM	71.84 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_794 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_794 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_794 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017861	1 retrocopy	retro_amel_194,
Bos taurus	ENSBTAG00000009969	7 retrocopies	retro_btau_1187, retro_btau_1239, retro_btau_1283, retro_btau_1515, retro_btau_764, retro_btau_776, retro_btau_85,
Canis familiaris	ENSCAFG00000019397	1 retrocopy	retro_cfam_449,
Equus caballus	ENSECAG00000023288	1 retrocopy	retro_ecab_524,
Felis catus	ENSFCAG00000007690	1 retrocopy	retro_fcat_248,
Homo sapiens	ENSG00000205937	1 retrocopy	retro_hsap_2911,
Gorilla gorilla	ENSGGOG00000014275	1 retrocopy	retro_ggor_2016,
Macropus eugenii	ENSMEUG00000008882	1 retrocopy	retro_meug_1996,
Myotis lucifugus	ENSMLUG00000016808	3 retrocopies	retro_mluc_2237, retro_mluc_2618, retro_mluc_643,
Macaca mulatta	ENSMMUG00000019238	1 retrocopy	retro_mmul_794 ,
Monodelphis domestica	ENSMODG00000015891	1 retrocopy	retro_mdom_1171,
Mus musculus	ENSMUSG00000034681	1 retrocopy	retro_mmus_173,
Otolemur garnettii	ENSOGAG00000031582	1 retrocopy	retro_ogar_3241,
Rattus norvegicus	ENSRNOG00000008703	4 retrocopies	retro_rnor_1537, retro_rnor_2135, retro_rnor_2988, retro_rnor_649,
Sarcophilus harrisii	ENSSHAG00000016951	1 retrocopy	retro_shar_390,
Ictidomys tridecemlineatus	ENSSTOG00000013200	1 retrocopy	retro_itri_1160,
Tupaia belangeri	ENSTBEG00000009098	8 retrocopies	retro_tbel_1262, retro_tbel_1851, retro_tbel_2132, retro_tbel_2154, retro_tbel_2216, retro_tbel_3193, retro_tbel_3286, retro_tbel_4688,
Tarsius syrichta	ENSTSYG00000001629	1 retrocopy	retro_tsyr_957,
Tursiops truncatus	ENSTTRG00000008220	7 retrocopies	retro_ttru_1010, retro_ttru_1033, retro_ttru_1558, retro_ttru_1808, retro_ttru_1809, retro_ttru_203, retro_ttru_986,