RetrogeneDB ID: retro_mmus_1440

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:16542284..16542739(+)
• Located in intron of: ENSMUSG00000022788

Retrocopy information

• Ensembl ID: ENSMUSG00000089861
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rps27a
• Ensembl ID: ENSMUSG00000020460
• Aliases: Rps27a, 0610006J14Rik, Uba52, Ubb, Ubc
• Description: ribosomal protein S27A [Source:MGI Symbol;Acc:MGI:1925544]

Sequence

>retro_mmus_1440
CAGAGTTTTATGAAGACCATTCTGGGAAGAGCACCATGCTCGAGGTTGAACCCCTGGACACCATAGAAAATGTAAAGGCC
AAGATCCAGGATAAGGAAGGACTTCCTCCTGATCAGTAGAGGCTGGTCTTTGCTGGTAAGCAGCTGGAAGATGGCCATAC
TTGTTTGACTACAACATTCAAAAGGAGTCCACCCTTCATCTTGTGTTGAGCCTTCTTGGTGGTGCTAAGAAAAGAAAGAA
GAAGTCTTACACCACTCCCAAGAAGAGTAAGCATAAGAGGAAGAAGGTTAAGTTGGCTCTGCTGAAAGGTGGATGAAAAT
GGCCAATCAGTTGACCTCATCCAGAGTGTCCTTCTGATGAGTGTGGTGCTGGAGTTATCATGGGAAGCCACTTTGACAGG
CACTGCTGTGGCAACTGTTGTCTGACTTAACTGCTTCAACAAACCAGAAGGCAAG

Alignment

ORF - retro_mmus_1440 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.88 %
• Parental protein coverage: 99.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  QIFVKTL-TGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRT-LSDYNIQKESTLHL
          Q.F.KT...GK...LEVEP.DTIENVKAKIQDKEG.PPDQ.RL.FAGKQLEDG.T.L.DYNIQKESTLHL
Retrocopy QSFMKTI<SGKSTMLEVEPLDTIENVKAKIQDKEGLPPDQ*RLVFAGKQLEDGHT<LFDYNIQKESTLHL

Parental  VLRLRGGAKKRKKKSYTTPKKNKHKRKKVKLAVLKYYK-VDENGK-ISRLRRECPSDECGAGVFMGSHFD
          VL.L.GGA...KK.........K....K.K...L...K.VDENG..IS....ECPSDECGAGV.MGSHFD
Retrocopy VLSLLGGA---KKRKKKSYTTPKKSKHKRKKVKLALLK>VDENGQ<IS*PHPECPSDECGAGVIMGSHFD

Parental  RHYCGKCCLT-YCFNKPEDK
          RH.CG.CCLT..CFNKPE.K
Retrocopy RHCCGNCCLT>NCFNKPEGK

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	54.37 RPM
SRP007412_cerebellum	0.04 RPM	28.27 RPM
SRP007412_heart	0.00 RPM	37.01 RPM
SRP007412_kidney	0.04 RPM	40.75 RPM
SRP007412_liver	0.03 RPM	49.78 RPM
SRP007412_testis	0.00 RPM	26.89 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1440 was not detected

EST

No EST(s) were mapped for retro_mmus_1440 retrocopy.

TSS

No TSS is located nearby retro_mmus_1440 retrocopy 5' end.

Lab

retro_mmus_1440 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1440 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 88 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004017	5 retrocopies	retro_amel_1565, retro_amel_175, retro_amel_598, retro_amel_661, retro_amel_844,
Canis familiaris	ENSCAFG00000023471	3 retrocopies	retro_cfam_1048, retro_cfam_640, retro_cfam_81,
Callithrix jacchus	ENSCJAG00000010052	5 retrocopies	retro_cjac_200, retro_cjac_229, retro_cjac_344, retro_cjac_74, retro_cjac_88,
Loxodonta africana	ENSLAFG00000023133	2 retrocopies	retro_lafr_1122, retro_lafr_185,
Macropus eugenii	ENSMEUG00000008917	13 retrocopies	retro_meug_107, retro_meug_1184, retro_meug_1460, retro_meug_1514, retro_meug_1544, retro_meug_1657, retro_meug_183, retro_meug_1866, retro_meug_209, retro_meug_521, retro_meug_594, retro_meug_937, retro_meug_94,
Myotis lucifugus	ENSMLUG00000017064	10 retrocopies	retro_mluc_1201, retro_mluc_1255, retro_mluc_1298, retro_mluc_1646, retro_mluc_1730, retro_mluc_1865, retro_mluc_1867, retro_mluc_2264, retro_mluc_37, retro_mluc_380,
Myotis lucifugus	ENSMLUG00000029449	1 retrocopy	retro_mluc_1585,
Macaca mulatta	ENSMMUG00000015563	8 retrocopies	retro_mmul_1198, retro_mmul_193, retro_mmul_2189, retro_mmul_222, retro_mmul_2470, retro_mmul_282, retro_mmul_606, retro_mmul_73,
Monodelphis domestica	ENSMODG00000001819	3 retrocopies	retro_mdom_1367, retro_mdom_1751, retro_mdom_205,
Mus musculus	ENSMUSG00000020460	19 retrocopies	retro_mmus_1074, retro_mmus_1268, retro_mmus_1440 , retro_mmus_1441, retro_mmus_1815, retro_mmus_1917, retro_mmus_2043, retro_mmus_2092, retro_mmus_2098, retro_mmus_2449, retro_mmus_2514, retro_mmus_2785, retro_mmus_2801, retro_mmus_2931, retro_mmus_306, retro_mmus_318, retro_mmus_3234, retro_mmus_3292, retro_mmus_3391,
Oryctolagus cuniculus	ENSOCUG00000003613	10 retrocopies	retro_ocun_1087, retro_ocun_1163, retro_ocun_1209, retro_ocun_1259, retro_ocun_1268, retro_ocun_1339, retro_ocun_164, retro_ocun_288, retro_ocun_381, retro_ocun_851,
Pongo abelii	ENSPPYG00000025871	1 retrocopy	retro_pabe_117,
Pan troglodytes	ENSPTRG00000011928	1 retrocopy	retro_ptro_32,
Rattus norvegicus	ENSRNOG00000004426	2 retrocopies	retro_rnor_117, retro_rnor_161,
Ictidomys tridecemlineatus	ENSSTOG00000009566	5 retrocopies	retro_itri_1583, retro_itri_1765, retro_itri_26, retro_itri_635, retro_itri_962,