RetrogeneDB ID: retro_mmus_3556

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:160036320..160037000(+)
• Located in intron of: ENSMUSG00000031303

Retrocopy information

• Ensembl ID: ENSMUSG00000082810
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Cfl1
• Ensembl ID: ENSMUSG00000056201
• Aliases: None
• Description: cofilin 1, non-muscle [Source:MGI Symbol;Acc:MGI:101757]

Sequence

>retro_mmus_3556
ATGGCCTCTGGTGTGGCTGTCTCTGATGGTGTCATCAAGGTGTTCAATGGTATGAAATTTCACAAGTCTTCAATGCCAGA
AAAAGTGAAGAAACACAAGAAGGCAGTGCTCTTTTGCCTGAGTAAGGACAAGAAGAACATTATCCTGGAGGAGGGCAAGG
AGATCCTGGTAGGAGATGTGGGGCAGAGTATGGATGACCCCTACACCATTTTGTCAAGATGCTGCCAGACAAGAACTGTA
GCTATGCTCTCTATAATGCAAACTATAAGACCAAGGAAGAGCAAGAAGGACCTGGTGTTCATCTTCTGGGCCCCTGAGAA
TGCACCCCTTAAAAGCAAAATGATCTATGCCAGCTCCAAGGATGCCATCAAGAAGTATCTGACAGGAAGCAAGCATGAAT
TACAATCTAACTGCTATGAGTAGGTCAAGGACCAATGCACCCTGGCAGAGAAACTAGGTGGCTGCACCATCATTTCCCTA
GAGGGCAAGCCTTTGTGAGCTACCTCCAGCCCCGGCCTGGAGCATCTAGCAGCCCCAGACATGCTCTTGGGTGTTGCAGG
CTGCTCCTTTCCTGTCAGGCTGGAACGGCTGGGGGGATCCCAGCACGGGGAGTGCTATCCCTTCACCCCAGTTGTGAAAC
ATCCCTCCCACCCCCTGGACTGTCCTTCTCCCTCCATCCC

Alignment

ORF - retro_mmus_3556 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MASGVAVSDGVIKVFNDMKVRKSSTPEEVKKRKKAVLFCLSEDKKNIILEEGKEILVGDVGQTVDDPYTT
          MASGVAVSDGVIKVFN.MK..KSS.PE.VKK.KKAVLFCLS.DKKNIILEEGKEILVGDVGQ..DDPYT.
Retrocopy MASGVAVSDGVIKVFNGMKFHKSSMPEKVKKHKKAVLFCLSKDKKNIILEEGKEILVGDVGQSMDDPYTI

Parental  -FVKMLPDKDCRYALYDATYETKE-SKKEDLVFIFWAPENAPLKSKMIYASSKDAIKKKLTGIKHELQAN
          .FVKMLPDK.C.YALY.A.Y.TKE.SKK.DLVFIFWAPENAPLKSKMIYASSKDAIKK.LTG.KHELQ.N
Retrocopy <FVKMLPDKNCSYALYNANYKTKE>SKK-DLVFIFWAPENAPLKSKMIYASSKDAIKKYLTGSKHELQSN

Parental  CYEEVKDRCTLAEKLGGSAVISLEGKPL-SHPAPCLEHL-NSPRPALGCCRLPLSCQTGGAGGIPAGGGL
          CYE.VKD.CTLAEKLGG...ISLEGKPL.....P.LEHL..SPR.ALGCCRL.LSCQ.G.AGGIPA.G.L
Retrocopy CYE*VKDQCTLAEKLGGCTIISLEGKPL*ATSSPGLEHL<SSPRHALGCCRLLLSCQAGTAGGIPARGVL

Parental  SLHPSCQTSLPPPGPSFSLHP
          SLHPSC.TSLPPPG.SFSLHP
Retrocopy SLHPSCETSLPPPGLSFSLHP

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	385.58 RPM
SRP007412_cerebellum	0.09 RPM	286.45 RPM
SRP007412_heart	0.03 RPM	80.81 RPM
SRP007412_kidney	0.10 RPM	152.73 RPM
SRP007412_liver	0.00 RPM	115.90 RPM
SRP007412_testis	0.00 RPM	106.85 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3556 was not detected

EST

No EST(s) were mapped for retro_mmus_3556 retrocopy.

TSS

No TSS is located nearby retro_mmus_3556 retrocopy 5' end.

Lab

retro_mmus_3556 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3556 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
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,
Felis catus	ENSFCAG00000013272	3 retrocopies	retro_fcat_1456, retro_fcat_303, retro_fcat_991,
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	ENSMMUG00000019016	5 retrocopies	retro_mmul_316, retro_mmul_493, retro_mmul_556, retro_mmul_667, retro_mmul_705,
Mus musculus	ENSMUSG00000015932	1 retrocopy	retro_mmus_3314,
Mus musculus	ENSMUSG00000056201	6 retrocopies	retro_mmus_1729, retro_mmus_2103, retro_mmus_3127, retro_mmus_3556 , retro_mmus_719, retro_mmus_970,
Mus musculus	ENSMUSG00000062929	1 retrocopy	retro_mmus_660,
Oryctolagus cuniculus	ENSOCUG00000025604	4 retrocopies	retro_ocun_1123, retro_ocun_1390, retro_ocun_324, retro_ocun_478,
Otolemur garnettii	ENSOGAG00000016503	8 retrocopies	retro_ogar_1442, retro_ogar_1581, retro_ogar_1648, retro_ogar_2192, retro_ogar_302, retro_ogar_405, retro_ogar_453, retro_ogar_828,
Rattus norvegicus	ENSRNOG00000020660	2 retrocopies	retro_rnor_1354, retro_rnor_693,
Tupaia belangeri	ENSTBEG00000016751	2 retrocopies	retro_tbel_153, retro_tbel_3085,