RetrogeneDB ID: retro_mmus_1568

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:36225999..36226271(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000060087
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Lsm5
• Ensembl ID: ENSMUSG00000091625
• Aliases: Lsm5, 2010208O10Rik, 2310034K10Rik
• Description: LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1913623]

Sequence

>retro_mmus_1568
ATGGTGGCTAACGCGACCACGAACCGTCCCAACTCCTGCCACTAGAACTTGTGGACAAATGTATAGGGTCAAGAATTCAC
ATTGTGATGAAGAGTGATAAAGAAATTGTCGGGACACTTCTAGGATTTGATGACTTTGTCAATATGGTGTTGGAAGATGT
CACAGAATTTGAAATTACACCAGAAGGAAGACGAATTACAAAATTAGATCAAATTCTACTAAATGGAAATAATATAACAA
TGCTGGTTCCCGGAGGAGAAGGGCCTGAAGTA

Alignment

ORF - retro_mmus_1568 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.83 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAANATTN-PSQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEITPEGRRITKL
          M.ANATTN.PSQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEITPEGRRITKL
Retrocopy MVANATTN<PSQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEITPEGRRITKL

Parental  DQILLNGNNITMLVPGGEGPEV
          DQILLNGNNITMLVPGGEGPEV
Retrocopy DQILLNGNNITMLVPGGEGPEV

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	1.59 RPM
SRP007412_cerebellum	0.00 RPM	1.69 RPM
SRP007412_heart	0.00 RPM	1.28 RPM
SRP007412_kidney	0.02 RPM	1.23 RPM
SRP007412_liver	0.00 RPM	1.37 RPM
SRP007412_testis	0.00 RPM	1.23 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1568 was not detected

EST

No EST(s) were mapped for retro_mmus_1568 retrocopy.

TSS

No TSS is located nearby retro_mmus_1568 retrocopy 5' end.

Lab

retro_mmus_1568 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1568 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006700	1 retrocopy	retro_amel_453,
Bos taurus	ENSBTAG00000002332	3 retrocopies	retro_btau_1012, retro_btau_1123, retro_btau_1313,
Callithrix jacchus	ENSCJAG00000009185	3 retrocopies	retro_cjac_1883, retro_cjac_2760, retro_cjac_3068,
Cavia porcellus	ENSCPOG00000010421	1 retrocopy	retro_cpor_607,
Equus caballus	ENSECAG00000018445	1 retrocopy	retro_ecab_809,
Echinops telfairi	ENSETEG00000018068	8 retrocopies	retro_etel_1305, retro_etel_1502, retro_etel_1907, retro_etel_198, retro_etel_2054, retro_etel_2193, retro_etel_454, retro_etel_964,
Loxodonta africana	ENSLAFG00000029579	3 retrocopies	retro_lafr_1000, retro_lafr_368, retro_lafr_922,
Mus musculus	ENSMUSG00000091625	4 retrocopies	retro_mmus_1568 , retro_mmus_423, retro_mmus_826, retro_mmus_837,
Nomascus leucogenys	ENSNLEG00000015268	1 retrocopy	retro_nleu_179,
Otolemur garnettii	ENSOGAG00000013892	3 retrocopies	retro_ogar_2727, retro_ogar_3062, retro_ogar_881,
Pongo abelii	ENSPPYG00000017661	1 retrocopy	retro_pabe_3449,
Pan troglodytes	ENSPTRG00000019057	1 retrocopy	retro_ptro_2862,
Pteropus vampyrus	ENSPVAG00000009786	1 retrocopy	retro_pvam_1410,
Rattus norvegicus	ENSRNOG00000042126	3 retrocopies	retro_rnor_1171, retro_rnor_567, retro_rnor_694,
Tupaia belangeri	ENSTBEG00000004876	11 retrocopies	retro_tbel_1043, retro_tbel_1107, retro_tbel_1217, retro_tbel_1323, retro_tbel_1549, retro_tbel_1865, retro_tbel_2203, retro_tbel_2908, retro_tbel_2956, retro_tbel_3330, retro_tbel_4335,
Tursiops truncatus	ENSTTRG00000004237	3 retrocopies	retro_ttru_1521, retro_ttru_1585, retro_ttru_874,