RetrogeneDB ID: retro_mmul_556

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:170167169..170167598(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4381
• Ensembl ID: ENSMMUG00000019016
• Aliases: CFL1, cofilin-1
• Description: cofilin-1 [Source:RefSeq peptide;Acc:NP_001253534]

Sequence

>retro_mmul_556
AAGGAGCACAAGTCTTCAACAGCAGAGGAGGTGAAGACACGTAAGAAGGTCGTGCTCTCTGCCTGAGTGGGGACGAGATC
ATTATCCTTGAGGAGGGCAGGGGGACCCTGGCAGGTGAAGTGGGGTAGGGTGTTGACGACTCCTACACCACAATTGTCAA
GATGCTGCCAGACAAGGACTGCCACTATGTCCTCTGTGACGCAACCTATGAGACCAAAGAGAGCCAAGAGGAGGACCTGG
TGTTTATCTTCTGAGCACCTCAGTCTGCACCCCTAAGAGTAGAATGATCTACGGCAGCTCCAAGGATGCCATCAAGAAGA
AGCTGACAGGGATCCTGCATGAATTACCAGCAAATGTCTATAGGAGGTCAAGGACCACTGTACCAGGCAGACAAGCTAGG
GGCAGCACTGTCATCTCCTGCAGGGCAAG

Alignment

ORF - retro_mmul_556 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.39 %
• Parental protein coverage: 97.99 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  KVRKSSTPEEVKKRKKAVL-FCLSEDKKNIILEEGKEILVGDVGQTVDDPYATFVKMLPDKDCRYALYDA
          K..KSST.EEVK.RKK.VL..CLS.D...IILEEG...L.G.VG..VDD.Y.T.VKMLPDKDC.Y.L.DA
Retrocopy KEHKSSTAEEVKTRKKVVL<LCLSGDEI-IILEEGRGTLAGEVG*GVDDSYTTIVKMLPDKDCHYVLCDA

Parental  TYETKESKKEDLVFIFWAPECAPL-KSKMIYASSKDAIKKKLTGIKHELQANCYE-EVKDRCT-LAEKLG
          TYETKES..EDLVFIF.AP..APL.KS.MIY.SSKDAIKKKLTGI.HEL.AN.Y..EVKD.CT..A.KLG
Retrocopy TYETKESQEEDLVFIF*APQSAPL<KSRMIYGSSKDAIKKKLTGILHELPANVYR<EVKDHCT<QADKLG

Parental  -GSAVIS-LEGK
          .GS.VIS.L.GK
Retrocopy <GSTVIS<LQGK

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	229.48 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	401.89 RPM
SRP007412_cerebellum	0.00 RPM	146.26 RPM
SRP007412_heart	0.00 RPM	71.96 RPM
SRP007412_kidney	0.00 RPM	130.28 RPM
SRP007412_liver	0.00 RPM	123.58 RPM
SRP007412_testis	0.00 RPM	82.13 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_556 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_556 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_556 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_287
Pan troglodytes	retro_ptro_236
Gorilla gorilla	retro_ggor_326
Pongo abelii	retro_pabe_386

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 73 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017334	2 retrocopies	retro_amel_583, retro_amel_816,
Canis familiaris	ENSCAFG00000024955	6 retrocopies	retro_cfam_1544, retro_cfam_366, retro_cfam_660, retro_cfam_67, retro_cfam_943, retro_cfam_964,
Callithrix jacchus	ENSCJAG00000001916	1 retrocopy	retro_cjac_347,
Equus caballus	ENSECAG00000019900	1 retrocopy	retro_ecab_442,
Felis catus	ENSFCAG00000013272	3 retrocopies	retro_fcat_1456, retro_fcat_303, retro_fcat_991,
Homo sapiens	ENSG00000172757	6 retrocopies	retro_hsap_2617, retro_hsap_287, retro_hsap_3333, retro_hsap_336, retro_hsap_384, retro_hsap_400,
Gorilla gorilla	ENSGGOG00000023183	5 retrocopies	retro_ggor_1832, retro_ggor_326, retro_ggor_357, retro_ggor_389, retro_ggor_397,
Myotis lucifugus	ENSMLUG00000024685	6 retrocopies	retro_mluc_1905, retro_mluc_2114, retro_mluc_216, retro_mluc_2218, retro_mluc_455, retro_mluc_507,
Macaca mulatta	ENSMMUG00000013786	1 retrocopy	retro_mmul_782,
Macaca mulatta	ENSMMUG00000019016	5 retrocopies	retro_mmul_316, retro_mmul_493, retro_mmul_556 , retro_mmul_667, retro_mmul_705,
Mustela putorius furo	ENSMPUG00000011502	2 retrocopies	retro_mputfur_1485, retro_mputfur_575,
Mus musculus	ENSMUSG00000056201	6 retrocopies	retro_mmus_1729, retro_mmus_2103, retro_mmus_3127, retro_mmus_3556, retro_mmus_719, retro_mmus_970,
Nomascus leucogenys	ENSNLEG00000005852	5 retrocopies	retro_nleu_139, retro_nleu_1494, retro_nleu_1571, retro_nleu_1777, retro_nleu_636,
Oryctolagus cuniculus	ENSOCUG00000025604	4 retrocopies	retro_ocun_1123, retro_ocun_1390, retro_ocun_324, retro_ocun_478,
Pongo abelii	ENSPPYG00000003047	5 retrocopies	retro_pabe_1732, retro_pabe_2747, retro_pabe_316, retro_pabe_325, retro_pabe_386,
Pan troglodytes	ENSPTRG00000003895	5 retrocopies	retro_ptro_1764, retro_ptro_2146, retro_ptro_236, retro_ptro_298, retro_ptro_306,
Rattus norvegicus	ENSRNOG00000020660	2 retrocopies	retro_rnor_1354, retro_rnor_693,
Ictidomys tridecemlineatus	ENSSTOG00000027968	4 retrocopies	retro_itri_144, retro_itri_1456, retro_itri_1734, retro_itri_685,
Tupaia belangeri	ENSTBEG00000016751	2 retrocopies	retro_tbel_153, retro_tbel_3085,
Tursiops truncatus	ENSTTRG00000016931	2 retrocopies	retro_ttru_1256, retro_ttru_598,