RetrogeneDB ID: retro_mmus_1390

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:39406574..39406876(-)
• Located in intron of: ENSMUSG00000037386

Retrocopy information

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

Parental gene information

• Parental gene symbol: Lsm3
• Ensembl ID: ENSMUSG00000034192
• Aliases: Lsm3, 1010001J12Rik, 2610005D18Rik, 6030401D18Rik, SMX4, USS2
• Description: LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1914928]

Sequence

>retro_mmus_1390
ATGGAGGACAACGGAGATCAGCAACAGACCACCGATAAGGGAGAGGAGCCCCTGGATCTTATCAGGCTCAGCTTGGATGA
GTGAATTTATGCGAAAATGAGAAATGACCAAGAGCTTCAAGGAAGAGTGCATGCTTATGATCAACATTTAAATATGGTCC
TGGGAGACATAGAAGAAACTGTGACGACGATAGAGAGTGATGAGGAGACATATGGAGAGAGAGATAAATCAACAAAACGA
AACATCCCATGCTCTTCTTCCAGGGAGATGGTGTTCTAGTCACCCCTCTGTTGAGAGGTGGC

Alignment

ORF - retro_mmus_1390 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.7 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADDVDQQQTTNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIEIDEET
          M.D..DQQQTT...EEPLDLIRLSLDE.IY.KMRND.EL.GR.HAYDQHLNM.LGD.EETVTTIE.DEET
Retrocopy MEDNGDQQQTTDKGEEPLDLIRLSLDE*IYAKMRNDQELQGRVHAYDQHLNMVLGDIEETVTTIESDEET

Parental  YEEIYKSTKRNI-PMLFVRGDGVVLVAPPLRVG
          Y.E..KSTKRNI.PMLF..GDG.VLV.P.LR.G
Retrocopy YGERDKSTKRNI<PMLFFQGDG-VLVTPLLRGG

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	0.07 RPM	10.56 RPM
SRP007412_cerebellum	0.09 RPM	9.12 RPM
SRP007412_heart	0.00 RPM	14.16 RPM
SRP007412_kidney	0.00 RPM	11.57 RPM
SRP007412_liver	0.00 RPM	4.01 RPM
SRP007412_testis	0.00 RPM	14.96 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1390 was not detected

EST

No EST(s) were mapped for retro_mmus_1390 retrocopy.

TSS

No TSS is located nearby retro_mmus_1390 retrocopy 5' end.

Lab

retro_mmus_1390 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1390 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 75 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009405	3 retrocopies	retro_amel_1756, retro_amel_659, retro_amel_838,
Callithrix jacchus	ENSCJAG00000016977	1 retrocopy	retro_cjac_54,
Cavia porcellus	ENSCPOG00000006671	1 retrocopy	retro_cpor_1445,
Dasypus novemcinctus	ENSDNOG00000018032	7 retrocopies	retro_dnov_1046, retro_dnov_135, retro_dnov_1728, retro_dnov_1818, retro_dnov_229, retro_dnov_230, retro_dnov_2408,
Echinops telfairi	ENSETEG00000016207	8 retrocopies	retro_etel_117, retro_etel_1678, retro_etel_1852, retro_etel_2131, retro_etel_472, retro_etel_521, retro_etel_598, retro_etel_833,
Gorilla gorilla	ENSGGOG00000010006	4 retrocopies	retro_ggor_104, retro_ggor_1699, retro_ggor_2068, retro_ggor_826,
Loxodonta africana	ENSLAFG00000023308	1 retrocopy	retro_lafr_1013,
Myotis lucifugus	ENSMLUG00000010677	4 retrocopies	retro_mluc_1148, retro_mluc_2306, retro_mluc_2337, retro_mluc_25,
Mus musculus	ENSMUSG00000034192	2 retrocopies	retro_mmus_1390 , retro_mmus_2446,
Nomascus leucogenys	ENSNLEG00000005079	6 retrocopies	retro_nleu_1138, retro_nleu_2934, retro_nleu_347, retro_nleu_739, retro_nleu_916, retro_nleu_958,
Oryctolagus cuniculus	ENSOCUG00000011088	1 retrocopy	retro_ocun_126,
Otolemur garnettii	ENSOGAG00000007659	6 retrocopies	retro_ogar_1031, retro_ogar_231, retro_ogar_242, retro_ogar_2490, retro_ogar_2818, retro_ogar_577,
Oreochromis niloticus	ENSONIG00000000370	1 retrocopy	retro_onil_12,
Pongo abelii	ENSPPYG00000013402	4 retrocopies	retro_pabe_1366, retro_pabe_1936, retro_pabe_2475, retro_pabe_874,
Pan troglodytes	ENSPTRG00000014650	5 retrocopies	retro_ptro_1125, retro_ptro_1161, retro_ptro_1619, retro_ptro_2020, retro_ptro_712,
Pteropus vampyrus	ENSPVAG00000016795	1 retrocopy	retro_pvam_646,
Rattus norvegicus	ENSRNOG00000008733	1 retrocopy	retro_rnor_1187,
Sus scrofa	ENSSSCG00000011601	6 retrocopies	retro_sscr_1134, retro_sscr_1140, retro_sscr_395, retro_sscr_396, retro_sscr_457, retro_sscr_64,
Ictidomys tridecemlineatus	ENSSTOG00000006842	1 retrocopy	retro_itri_613,
Tupaia belangeri	ENSTBEG00000001050	11 retrocopies	retro_tbel_1034, retro_tbel_1343, retro_tbel_2860, retro_tbel_2969, retro_tbel_3184, retro_tbel_331, retro_tbel_3422, retro_tbel_3457, retro_tbel_414, retro_tbel_4663, retro_tbel_794,
Tursiops truncatus	ENSTTRG00000011197	1 retrocopy	retro_ttru_601,