RetrogeneDB ID: retro_mmus_3203

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:57520155..57520888(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: 2700060E02Rik
• Ensembl ID: ENSMUSG00000021807
• Aliases: None
• Description: RIKEN cDNA 2700060E02 gene [Source:MGI Symbol;Acc:MGI:1915295]

Sequence

>retro_mmus_3203
ATGTTCCGACACAAGCTCACAGCCCTGGATTACCTCAACACTTCGGGCTTCAACTGCAAAGATGAAACAGAATTTAGAAA
CTGTATTGTTTGGCTTGAAGACCAGAAAATCAGACACTATGAGATCGAAGATAGAGGTAACTTGAGAAACATCCCCGGTA
GTGACTGGCCCAAGTTCTTTGAAAAGTATCTCAGAGATATTAACTGTCCTTTCAAGACTCGGAATCGGCAAGAAGCAATT
GACTGGCTTGTTGGTTTAGCTGTTAGACTTGAACATGAAGATAACACTGAAAACTACAAGGACTTAGTACCTGATAACAA
GAAAAATACTGACAACGCAGCTAAAAATGCAGAGCCACTGATCAACTCGGACGTAAATTATCCTGACTTTAAGGCTGGTG
TCACAGCTCTGGCTAACCTCCTTCAGATTCAGCGTCATGATGACTACTTGGTAATGCTTAAGGCAATTGGCATTTTGGCT
TAAGAACATCTAACACAGGATGCAGTTGCCAAAGCAAATACAACAAAAGGCAGCTGACCTGTTGCTTTAGACAAACATAT
TCTTGGCTCTGACAAAGGCGATGCACTTCTTAATGAAGCTGCTCAGATCCGTGCAGTTGCTGCACATAGAAGAGCTCTGA
GAGCTACAGACAAACATTAATGAAGCCACAGTAGCGGTTCAAGCCGTCATTGCTGATCCAAAGACAGACCACAGACTGGG
GAAGGTAGGGAGA

Alignment

ORF - retro_mmus_3203 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.67 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFRRKLTALDYHNPSGFNCKDETEFRNFIVWLEDQKIRHYKIEDRGNLRNIHSSDWPKFFEKYLKDVNCP
          MFR.KLTALDY.N.SGFNCKDETEFRN.IVWLEDQKIRHY.IEDRGNLRNI..SDWPKFFEKYL.D.NCP
Retrocopy MFRHKLTALDYLNTSGFNCKDETEFRNCIVWLEDQKIRHYEIEDRGNLRNIPGSDWPKFFEKYLRDINCP

Parental  FKIQDRQEAIDWLLGLAVRLEYGDNAEKYKDLVPDNRKNTDNAAKNAEPLINLDVNNPDFKAGVMALANL
          FK...RQEAIDWL.GLAVRLE..DN.E.YKDLVPDN.KNTDNAAKNAEPLIN.DVN.PDFKAGV.ALANL
Retrocopy FKTRNRQEAIDWLVGLAVRLEHEDNTENYKDLVPDNKKNTDNAAKNAEPLINSDVNYPDFKAGVTALANL

Parental  LQIQRHDDYLVMLKAIRILVQERLTQDAVAKANQTKEGLPVALEKHILGFDTGDAVLNEAAQI-LRLLHI
          LQIQRHDDYLVMLKAI.IL..E.LTQDAVAKAN.TK...PVAL.KHILG.D.GDA.LNEAAQI...LLHI
Retrocopy LQIQRHDDYLVMLKAIGILA*EHLTQDAVAKANTTKGS*PVALDKHILGSDKGDALLNEAAQI>VQLLHI

Parental  EELRELQTKINEAIVAVQAIIADPKTDHRLGKVGR
          EEL.ELQT.INEA.VAVQA.IADPKTDHRLGKVGR
Retrocopy EEL*ELQTNINEATVAVQAVIADPKTDHRLGKVGR

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	0.02 RPM	32.64 RPM
SRP007412_cerebellum	0.17 RPM	21.80 RPM
SRP007412_heart	0.06 RPM	34.21 RPM
SRP007412_kidney	0.02 RPM	30.43 RPM
SRP007412_liver	0.03 RPM	27.28 RPM
SRP007412_testis	3.02 RPM	40.89 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_mmus_3203 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	8:57519776..57522073

EST

No EST(s) were mapped for retro_mmus_3203 retrocopy.

TSS

No TSS is located nearby retro_mmus_3203 retrocopy 5' end.

Lab

retro_mmus_3203 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3203 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 29 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002083	2 retrocopies	retro_amel_224, retro_amel_302,
Canis familiaris	ENSCAFG00000014648	4 retrocopies	retro_cfam_1025, retro_cfam_2042, retro_cfam_237, retro_cfam_734,
Callithrix jacchus	ENSCJAG00000006926	3 retrocopies	retro_cjac_1262, retro_cjac_1947, retro_cjac_3207,
Cavia porcellus	ENSCPOG00000001317	6 retrocopies	retro_cpor_1041, retro_cpor_1177, retro_cpor_1239, retro_cpor_1247, retro_cpor_517, retro_cpor_541,
Dasypus novemcinctus	ENSDNOG00000003248	3 retrocopies	retro_dnov_458, retro_dnov_572, retro_dnov_609,
Dipodomys ordii	ENSDORG00000012335	1 retrocopy	retro_dord_619,
Equus caballus	ENSECAG00000012600	1 retrocopy	retro_ecab_483,
Erinaceus europaeus	ENSEEUG00000015583	1 retrocopy	retro_eeur_366,
Felis catus	ENSFCAG00000002663	3 retrocopies	retro_fcat_1160, retro_fcat_1415, retro_fcat_948,
Homo sapiens	ENSG00000087302	1 retrocopy	retro_hsap_2307,
Loxodonta africana	ENSLAFG00000003162	1 retrocopy	retro_lafr_301,
Microcebus murinus	ENSMICG00000008720	1 retrocopy	retro_mmur_857,
Myotis lucifugus	ENSMLUG00000008643	6 retrocopies	retro_mluc_1228, retro_mluc_1518, retro_mluc_1834, retro_mluc_2610, retro_mluc_456, retro_mluc_676,
Macaca mulatta	ENSMMUG00000018200	2 retrocopies	retro_mmul_1045, retro_mmul_2025,
Monodelphis domestica	ENSMODG00000013211	1 retrocopy	retro_mdom_1296,
Mustela putorius furo	ENSMPUG00000005253	6 retrocopies	retro_mputfur_1333, retro_mputfur_1421, retro_mputfur_203, retro_mputfur_328, retro_mputfur_655, retro_mputfur_797,
Mus musculus	ENSMUSG00000021807	2 retrocopies	retro_mmus_140, retro_mmus_3203 ,
Nomascus leucogenys	ENSNLEG00000012406	1 retrocopy	retro_nleu_2749,
Oryctolagus cuniculus	ENSOCUG00000014681	1 retrocopy	retro_ocun_221,
Otolemur garnettii	ENSOGAG00000013232	5 retrocopies	retro_ogar_1060, retro_ogar_1856, retro_ogar_2351, retro_ogar_2976, retro_ogar_3192,
Ochotona princeps	ENSOPRG00000016352	2 retrocopies	retro_opri_257, retro_opri_884,
Pongo abelii	ENSPPYG00000005814	1 retrocopy	retro_pabe_1980,
Pan troglodytes	ENSPTRG00000006344	1 retrocopy	retro_ptro_1631,
Pteropus vampyrus	ENSPVAG00000013392	1 retrocopy	retro_pvam_1088,
Sus scrofa	ENSSSCG00000005029	1 retrocopy	retro_sscr_1093,
Tupaia belangeri	ENSTBEG00000013898	5 retrocopies	retro_tbel_2579, retro_tbel_4337, retro_tbel_683, retro_tbel_880, retro_tbel_881,
Tarsius syrichta	ENSTSYG00000004528	6 retrocopies	retro_tsyr_1183, retro_tsyr_1289, retro_tsyr_1353, retro_tsyr_157, retro_tsyr_541, retro_tsyr_939,
Tursiops truncatus	ENSTTRG00000005721	1 retrocopy	retro_ttru_83,
Vicugna pacos	ENSVPAG00000011443	1 retrocopy	retro_vpac_142,