RetrogeneDB ID: retro_mmul_717

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099214741134:11100..11745(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.3260
• Ensembl ID: ENSMMUG00000018653
• Aliases: None
• Description: None

Sequence

>retro_mmul_717
CAGAAAGCTCTGCGCATGCGCTTGGAGGGCGCCATCAAAGTGCGCAGGTGCGGGACGAGCTGACCTAGGCAGGACCCGCC
TGGAGATGCAGATCCATGGCCTGAAAGAGGAGCTGGCGTCCCTGAAAAACAACCACGAGGAGGAAGTCGGTGGCTGAGGG
GCCAAGCGGGAGGCCAGGTCAGTGTGGAGGTGATTCGGCTTCCGGCACCGATCTGGCCGAGATCCCGAGTGACCTGCAAG
CCAATGTGAGGCCATGGCGGATCGGAACCGGAAGGAGCTGACGTCGGGTTCACCAGCGGGGCTGAGGAGCTGAACTGGGA
GGTCGCTGGCCACACGAAGCAGCTCCAGATGAGCAGGTCCAATGTCACTCACCTGTGGGGCACCCTCCAGGGTCTTGAGA
TTGAGCTGCAGTCGCAGCTAGGCCTGAAAGCTGCCTTGGAAGCCACACTGGTGGAAACTGCGGTGCGCTTTGGTGCCCAG
CTGGTGCAGATCCGGGCTCTGAGGAGACGTATTGAAGGGCCGGTTGGCCACTGTGTGAGCTGACAGCGGCAGGGGCAGGA
GGTCGCCACCTACCGCAGCCTGCTCAAGAGCCAGGGAGATCATTCCAACAACCTCTCCACCTCCAAGGGCCTCTGAGGCG
GCAGG

Alignment

ORF - retro_mmul_717 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.22 %
• Parental protein coverage: 54. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  EQALRMSVEADINGLRR-VLDELT-LARTDLEMQIEGLKEELAYLKKNHEEEISV-LRGQVGGQVSVEV-
          ..ALRM..E..I...RR.V.DELT.L.RT.LEMQI.GLKEELA.LK.NHEEE....LRGQ.GGQVSVEV.
Retrocopy QKALRMRLEGAIK-VRR<VRDELT<LGRTRLEMQIHGLKEELASLKNNHEEEVGG<LRGQAGGQVSVEV<

Parental  DSAPGTDLAKILSDMR-SQYEVMAEQNRKD-AEAWFTSRTEELNREVAGHTEQLQISRSEVTDLRRTLQG
          DSA.GTDLA.I.SD...SQ.E.MA..NRK..A...FTS..EELN.EVAGHT.QLQ.SRS.VT.L..TLQG
Retrocopy DSASGTDLAEIPSDLQ<SQCEAMADRNRKE<ADVGFTSGAEELNWEVAGHTKQLQMSRSNVTHLWGTLQG

Parental  LEIELQSQLSMKAALEDTLAETEARFGAQLAHIQALISGVEAQLGDVRADSERQNQE---YQRLMDIKSR
          LEIELQSQL..KAALE.TL.ET..RFGAQL..I.AL....E...G.......RQ.QE...Y..L......
Retrocopy LEIELQSQLGLKAALEATLVETAVRFGAQLVQIRALRRRIEGPVGHC-VS*QRQGQEVATYRSLLKSQGD

Parental  LEQEIATYRSLLEGQ
          ......T...L..G.
Retrocopy HSNNLSTSKGL*GGR

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	1.79 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	2.54 RPM
SRP007412_cerebellum	0.00 RPM	0.39 RPM
SRP007412_heart	0.00 RPM	15.07 RPM
SRP007412_kidney	0.00 RPM	10.33 RPM
SRP007412_liver	0.00 RPM	0.99 RPM
SRP007412_testis	0.04 RPM	1.24 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_717 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_717 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_717 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000029756	9 retrocopies	retro_cjac_1151, retro_cjac_1812, retro_cjac_2347, retro_cjac_2646, retro_cjac_3108, retro_cjac_3198, retro_cjac_3237, retro_cjac_3358, retro_cjac_633,
Equus caballus	ENSECAG00000014086	2 retrocopies	retro_ecab_76, retro_ecab_931,
Echinops telfairi	ENSETEG00000007881	6 retrocopies	retro_etel_1217, retro_etel_1319, retro_etel_191, retro_etel_480, retro_etel_685, retro_etel_95,
Homo sapiens	ENSG00000171345	3 retrocopies	retro_hsap_3486, retro_hsap_585, retro_hsap_959,
Gorilla gorilla	ENSGGOG00000016901	3 retrocopies	retro_ggor_2352, retro_ggor_518, retro_ggor_773,
Macropus eugenii	ENSMEUG00000016158	3 retrocopies	retro_meug_1860, retro_meug_403, retro_meug_826,
Macaca mulatta	ENSMMUG00000018653	4 retrocopies	retro_mmul_1770, retro_mmul_717 , retro_mmul_774, retro_mmul_790,
Nomascus leucogenys	ENSNLEG00000010787	3 retrocopies	retro_nleu_1609, retro_nleu_2204, retro_nleu_800,
Oryctolagus cuniculus	ENSOCUG00000016132	1 retrocopy	retro_ocun_1884,
Otolemur garnettii	ENSOGAG00000024306	1 retrocopy	retro_ogar_1301,
Ochotona princeps	ENSOPRG00000007908	2 retrocopies	retro_opri_337, retro_opri_673,
Pongo abelii	ENSPPYG00000008416	3 retrocopies	retro_pabe_2880, retro_pabe_603, retro_pabe_820,
Pan troglodytes	ENSPTRG00000009168	3 retrocopies	retro_ptro_2074, retro_ptro_2359, retro_ptro_430,
Ictidomys tridecemlineatus	ENSSTOG00000014403	2 retrocopies	retro_itri_1514, retro_itri_697,