RetrogeneDB ID: retro_mmus_3723

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:159584785..159585109(-)
• Located in intron of: ENSMUSG00000044150

Retrocopy information

• Ensembl ID: ENSMUSG00000082693
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Lamtor5
• Ensembl ID: ENSMUSG00000087260
• Aliases: Lamtor5, 1110003H18Rik, Hbxip, XIP
• Description: late endosomal/lysosomal adaptor, MAPK and MTOR activator 5 [Source:MGI Symbol;Acc:MGI:1915826]

Sequence

>retro_mmus_3723
GGAGGAAGTGTTTTGCTGCGGGGTCCTGGCCCGGGGCAGACAGCCTGTGGGATGGAGGCAACTTTGGAGCAGCATTTGGA
GGACACAATGAAGAATCCATCCATTGTTGGAGTCCTATGCACAGATTCACAAGGACTTAATCTGGGCTGCCGTGGTACCC
TGTCCGATGAGCATGCTGGAGTGATAACTGTTCTAGCCCAGCAGGCAGCTAAGCTAACCTCTGACCCCACCGACATCCCT
GTGGTATGTTTAGAATCAGATAATGGGAACATTATGATCCAGAAACACGATGGCATCACAGTGGCTGTGCACAAAATGGC
CTCT

Alignment

ORF - retro_mmus_3723 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.3 %
• Parental protein coverage: 74.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGSVLLRGPGLGRTACGMEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDEHAGVISVLAQQAA
          GGSVLLRGPG.G.TACGMEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDEHAGVI.VLAQQAA
Retrocopy GGSVLLRGPGPGQTACGMEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDEHAGVITVLAQQAA

Parental  RLTSDPTDIPVVCLESDNGNIMIQKHDGITVAVHKMAS
          .LTSDPTDIPVVCLESDNGNIMIQKHDGITVAVHKMAS
Retrocopy KLTSDPTDIPVVCLESDNGNIMIQKHDGITVAVHKMAS

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	0.28 RPM	17.45 RPM
SRP007412_cerebellum	0.43 RPM	17.89 RPM
SRP007412_heart	0.22 RPM	20.92 RPM
SRP007412_kidney	1.21 RPM	33.03 RPM
SRP007412_liver	0.41 RPM	12.10 RPM
SRP007412_testis	0.82 RPM	11.71 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3723 was not detected

EST

No EST(s) were mapped for retro_mmus_3723 retrocopy.

TSS

No TSS is located nearby retro_mmus_3723 retrocopy 5' end.

Lab

retro_mmus_3723 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3723 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 58 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011504	2 retrocopies	retro_amel_118, retro_amel_974,
Bos taurus	ENSBTAG00000014970	3 retrocopies	retro_btau_1505, retro_btau_1755, retro_btau_71,
Callithrix jacchus	ENSCJAG00000003438	1 retrocopy	retro_cjac_2918,
Dipodomys ordii	ENSDORG00000005672	3 retrocopies	retro_dord_147, retro_dord_642, retro_dord_775,
Equus caballus	ENSECAG00000021821	1 retrocopy	retro_ecab_1026,
Homo sapiens	ENSG00000134248	1 retrocopy	retro_hsap_162,
Gorilla gorilla	ENSGGOG00000016522	1 retrocopy	retro_ggor_247,
Microcebus murinus	ENSMICG00000005264	4 retrocopies	retro_mmur_1114, retro_mmur_152, retro_mmur_422, retro_mmur_454,
Myotis lucifugus	ENSMLUG00000007198	2 retrocopies	retro_mluc_512, retro_mluc_708,
Macaca mulatta	ENSMMUG00000015023	4 retrocopies	retro_mmul_164, retro_mmul_2452, retro_mmul_440, retro_mmul_499,
Mustela putorius furo	ENSMPUG00000003833	5 retrocopies	retro_mputfur_1013, retro_mputfur_1020, retro_mputfur_1187, retro_mputfur_1387, retro_mputfur_921,
Mus musculus	ENSMUSG00000087260	3 retrocopies	retro_mmus_1061, retro_mmus_1901, retro_mmus_3723 ,
Oryctolagus cuniculus	ENSOCUG00000002449	2 retrocopies	retro_ocun_1880, retro_ocun_356,
Otolemur garnettii	ENSOGAG00000033478	2 retrocopies	retro_ogar_1388, retro_ogar_3454,
Ochotona princeps	ENSOPRG00000004283	5 retrocopies	retro_opri_138, retro_opri_199, retro_opri_488, retro_opri_567, retro_opri_716,
Pan troglodytes	ENSPTRG00000001078	2 retrocopies	retro_ptro_155, retro_ptro_436,
Sus scrofa	ENSSSCG00000006807	1 retrocopy	retro_sscr_986,
Ictidomys tridecemlineatus	ENSSTOG00000003401	5 retrocopies	retro_itri_1196, retro_itri_154, retro_itri_198, retro_itri_587, retro_itri_86,
Tupaia belangeri	ENSTBEG00000009117	5 retrocopies	retro_tbel_1220, retro_tbel_1427, retro_tbel_1756, retro_tbel_2289, retro_tbel_2329,
Tarsius syrichta	ENSTSYG00000006011	5 retrocopies	retro_tsyr_305, retro_tsyr_306, retro_tsyr_318, retro_tsyr_560, retro_tsyr_870,
Tursiops truncatus	ENSTTRG00000001319	1 retrocopy	retro_ttru_602,