RetrogeneDB ID: retro_mmus_3223

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:81024035..81024278(-)
• Located in intron of: ENSMUSG00000037982

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mrps36
• Ensembl ID: ENSMUSG00000061474
• Aliases: Mrps36, 1110018B13Rik, S36mt
• Description: mitochondrial ribosomal protein S36 [Source:MGI Symbol;Acc:MGI:1913378]

Sequence

>retro_mmus_3223
ATGGGTACCAAGAAGGTGTTGGCCAGCAGAGATACTCAGATAGTTAAGGTACACACTCTTCAACATGATTCTCTAAGAAA
TGATCCTAAACCCAGTACATGAGAAGCTCTTACATCAGCAGGGCTTCCATCTCATGCTTCTGGAATTTCCCAGCATTCTA
AGGGAAGCTGGTCACCAGATCTCCTGAGACAATGGAATCCACTAGACATTGAAGAAATAACAAAAATATTACCTTCAAAC
TAT

Alignment

ORF - retro_mmus_3223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.01 %
• Parental protein coverage: 81.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGSKMASATRVVQVVKPHAPLIKFPNRRDKPKLSASEALGSAALPSHSSAISQHSKGSTSPDLLMHQGPP
          MG.K...A.R..Q.VK.H.........R..PK.S..EAL.SA.LPSH.S.ISQHSKGS.SPDLL....P.
Retrocopy MGTKKVLASRDTQIVKVHT--LQHDSLRNDPKPST*EALTSAGLPSHASGISQHSKGSWSPDLLRQWNPL

Parental  DTAEIIKSLPQKY
          D..EI.K.LP..Y
Retrocopy DIEEITKILPSNY

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	3.46 RPM
SRP007412_cerebellum	0.04 RPM	3.08 RPM
SRP007412_heart	0.00 RPM	14.10 RPM
SRP007412_kidney	0.00 RPM	7.95 RPM
SRP007412_liver	0.05 RPM	3.74 RPM
SRP007412_testis	0.14 RPM	6.91 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3223 was not detected

EST

No EST(s) were mapped for retro_mmus_3223 retrocopy.

TSS

No TSS is located nearby retro_mmus_3223 retrocopy 5' end.

Lab

retro_mmus_3223 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3223 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 67 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003161	2 retrocopies	retro_amel_1838, retro_amel_565,
Callithrix jacchus	ENSCJAG00000016092	2 retrocopies	retro_cjac_3202, retro_cjac_45,
Dipodomys ordii	ENSDORG00000007063	1 retrocopy	retro_dord_110,
Echinops telfairi	ENSETEG00000019493	2 retrocopies	retro_etel_1624, retro_etel_625,
Felis catus	ENSFCAG00000031782	1 retrocopy	retro_fcat_724,
Homo sapiens	ENSG00000134056	2 retrocopies	retro_hsap_2750, retro_hsap_823,
Loxodonta africana	ENSLAFG00000007932	2 retrocopies	retro_lafr_1243, retro_lafr_598,
Monodelphis domestica	ENSMODG00000019701	1 retrocopy	retro_mdom_1559,
Mus musculus	ENSMUSG00000061474	4 retrocopies	retro_mmus_105, retro_mmus_123, retro_mmus_3223 , retro_mmus_753,
Nomascus leucogenys	ENSNLEG00000004071	4 retrocopies	retro_nleu_1545, retro_nleu_196, retro_nleu_2243, retro_nleu_257,
Oryctolagus cuniculus	ENSOCUG00000005261	2 retrocopies	retro_ocun_1057, retro_ocun_1109,
Otolemur garnettii	ENSOGAG00000024260	9 retrocopies	retro_ogar_1166, retro_ogar_1716, retro_ogar_2238, retro_ogar_2363, retro_ogar_2629, retro_ogar_3382, retro_ogar_711, retro_ogar_790, retro_ogar_869,
Ochotona princeps	ENSOPRG00000011392	1 retrocopy	retro_opri_587,
Pongo abelii	ENSPPYG00000015524	3 retrocopies	retro_pabe_2219, retro_pabe_735, retro_pabe_917,
Pan troglodytes	ENSPTRG00000016944	4 retrocopies	retro_ptro_1858, retro_ptro_2038, retro_ptro_573, retro_ptro_690,
Pteropus vampyrus	ENSPVAG00000010843	1 retrocopy	retro_pvam_174,
Rattus norvegicus	ENSRNOG00000048862	2 retrocopies	retro_rnor_1792, retro_rnor_2014,
Ictidomys tridecemlineatus	ENSSTOG00000021863	2 retrocopies	retro_itri_1039, retro_itri_938,
Tupaia belangeri	ENSTBEG00000012048	22 retrocopies	retro_tbel_1313, retro_tbel_1494, retro_tbel_1527, retro_tbel_224, retro_tbel_2404, retro_tbel_2661, retro_tbel_2755, retro_tbel_2762, retro_tbel_2924, retro_tbel_2934, retro_tbel_3239, retro_tbel_3240, retro_tbel_359, retro_tbel_3891, retro_tbel_3893, retro_tbel_3941, retro_tbel_4124, retro_tbel_4429, retro_tbel_4515, retro_tbel_4543, retro_tbel_4592, retro_tbel_702,