RetrogeneDB ID: retro_mmus_3682

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:105989903..105990124(-)
• Located in intron of: ENSMUSG00000031232

Retrocopy information

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

Parental gene information

• Parental gene symbol: Snrpe
• Ensembl ID: ENSMUSG00000090553
• Aliases: Snrpe, AL022645, C76690, SME
• Description: small nuclear ribonucleoprotein E [Source:MGI Symbol;Acc:MGI:98346]

Sequence

>retro_mmus_3682
AACCGCATCTTCAGATACTTGCAAAATAGAATTTGAATTCATGTGTGCCTGTATGAGCAAGTGAATATTCGGATAGAGGG
CTGATTATTGGCTTTGATAAGTGCACGAACCTCAAATTAGATGATGCAGAAGAGGTTCATTCTAAAACAAAGTCAGGAAA
ACAACTGGGTCGGATCGTGCTAAAAGGAGATAATACTACTCTGCTCCAAAGTGTTTCCAAC

Alignment

ORF - retro_mmus_3682 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.67 %
• Parental protein coverage: 80.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NLIFRYLQNRSRIQVWLYEQVNMRIEG-CIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDNITLL
          N.IFRYLQNR..I.V.LYEQVN.RIEG..IIGFD...NL.LDDAEE.HSKTKS.KQLGRI.LKGDN.TLL
Retrocopy NRIFRYLQNRI*IHVCLYEQVNIRIEG<LIIGFDKCTNLKLDDAEEVHSKTKSGKQLGRIVLKGDNTTLL

Parental  QSVSN
          QSVSN
Retrocopy QSVSN

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	11.21 RPM
SRP007412_cerebellum	0.00 RPM	9.25 RPM
SRP007412_heart	0.06 RPM	11.61 RPM
SRP007412_kidney	0.06 RPM	14.80 RPM
SRP007412_liver	0.00 RPM	11.14 RPM
SRP007412_testis	0.00 RPM	9.88 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3682 was not detected

EST

No EST(s) were mapped for retro_mmus_3682 retrocopy.

TSS

No TSS is located nearby retro_mmus_3682 retrocopy 5' end.

Lab

retro_mmus_3682 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3682 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 109 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000882	8 retrocopies	retro_amel_1112, retro_amel_1206, retro_amel_1211, retro_amel_1293, retro_amel_1517, retro_amel_1530, retro_amel_185, retro_amel_412,
Callithrix jacchus	ENSCJAG00000006735	1 retrocopy	retro_cjac_3163,
Dasypus novemcinctus	ENSDNOG00000004490	24 retrocopies	retro_dnov_1009, retro_dnov_1141, retro_dnov_122, retro_dnov_1223, retro_dnov_1312, retro_dnov_1314, retro_dnov_1362, retro_dnov_1438, retro_dnov_163, retro_dnov_191, retro_dnov_2398, retro_dnov_2671, retro_dnov_360, retro_dnov_414, retro_dnov_513, retro_dnov_579, retro_dnov_796, retro_dnov_828, retro_dnov_898, retro_dnov_900, retro_dnov_902, retro_dnov_93, retro_dnov_967, retro_dnov_983,
Echinops telfairi	ENSETEG00000014015	24 retrocopies	retro_etel_1136, retro_etel_1244, retro_etel_138, retro_etel_1443, retro_etel_1530, retro_etel_1636, retro_etel_1739, retro_etel_1781, retro_etel_1947, retro_etel_2143, retro_etel_234, retro_etel_258, retro_etel_310, retro_etel_377, retro_etel_466, retro_etel_546, retro_etel_56, retro_etel_579, retro_etel_581, retro_etel_582, retro_etel_76, retro_etel_776, retro_etel_799, retro_etel_80,
Gorilla gorilla	ENSGGOG00000000755	7 retrocopies	retro_ggor_1462, retro_ggor_1626, retro_ggor_1700, retro_ggor_2221, retro_ggor_228, retro_ggor_2892, retro_ggor_91,
Myotis lucifugus	ENSMLUG00000013244	8 retrocopies	retro_mluc_1639, retro_mluc_1650, retro_mluc_1994, retro_mluc_2045, retro_mluc_2088, retro_mluc_2326, retro_mluc_85, retro_mluc_919,
Monodelphis domestica	ENSMODG00000028394	3 retrocopies	retro_mdom_1164, retro_mdom_1790, retro_mdom_1865,
Mustela putorius furo	ENSMPUG00000011642	7 retrocopies	retro_mputfur_1078, retro_mputfur_1527, retro_mputfur_1634, retro_mputfur_53, retro_mputfur_638, retro_mputfur_729, retro_mputfur_949,
Mus musculus	ENSMUSG00000090553	10 retrocopies	retro_mmus_1527, retro_mmus_1597, retro_mmus_1704, retro_mmus_2090, retro_mmus_2788, retro_mmus_2953, retro_mmus_296, retro_mmus_3001, retro_mmus_3682 , retro_mmus_898,
Pongo abelii	ENSPPYG00000000326	8 retrocopies	retro_pabe_1375, retro_pabe_20, retro_pabe_2023, retro_pabe_228, retro_pabe_3015, retro_pabe_3620, retro_pabe_56, retro_pabe_610,
Sorex araneus	ENSSARG00000003311	9 retrocopies	retro_sara_171, retro_sara_173, retro_sara_183, retro_sara_214, retro_sara_219, retro_sara_37, retro_sara_664, retro_sara_697, retro_sara_750,