RetrogeneDB ID: retro_mmus_3342

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:59471761..59472233(-)
• Located in intron of: ENSMUSG00000025234

Retrocopy information

• Ensembl ID: ENSMUSG00000090516
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rps11
• Ensembl ID: ENSMUSG00000003429
• Aliases: None
• Description: ribosomal protein S11 [Source:MGI Symbol;Acc:MGI:1351329]

Sequence

>retro_mmus_3342
ATGGCGAACATTCAGACAGAGCGTGCTTACCAAAAGCAGCCTACGATCTTTCAAAACAAGAAGTGGGTTCTGCTGGGAGA
AACCGGCAAGGAAAAACTCCCTCGGTACTACAAGAACATCAGTCTAGGCTTCAGGACGCCCAAAGAGGCCATCAAGGGCA
CCTACATAGACAAGAAATGCCCCTTCACTGGTAACGTCTCCATCTGTGGTCGGATCCTGTCTGGTGTCGTGACGAAGATG
AAGATGCAGAGGACAGTCGTCATCCACCGGGACTATCTCCATTACATCTGAAAGTACAATCGCTTTGAGAAGTGTCACAA
GAACATGTCTGCACCTGCCCCCCTGTTTCAGGGATGTACAGATCGGAGACATTGTCACAGTTGGAGAGTGCAGGCCCCTG
AGCAAGACTGTGCGATTCAATGTGCTCAAGGTCACCAAGGCTGCTGGCACCAAGAAGCAGTTTCAGAAGTTC

Alignment

ORF - retro_mmus_3342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.94 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKCPFTGNVSIRG
          MA.IQTERAYQKQPTIFQNKK.VLLGETGKEKLPRYYKNI.LGF.TPKEAI.GTYIDKKCPFTGNVSI.G
Retrocopy MANIQTERAYQKQPTIFQNKKWVLLGETGKEKLPRYYKNISLGFRTPKEAIKGTYIDKKCPFTGNVSICG

Parental  RILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCF-RDVQIGDIVTVGECRPLSKTVR
          RILSGVVTKMKMQRT.VI.RDYLHYI.KYNRFEK.HKNMS....P.F.RDVQIGDIVTVGECRPLSKTVR
Retrocopy RILSGVVTKMKMQRTVVIHRDYLHYI*KYNRFEKCHKNMSAP-APLF>RDVQIGDIVTVGECRPLSKTVR

Parental  FNVLKVTKAAGTKKQFQKF
          FNVLKVTKAAGTKKQFQKF
Retrocopy FNVLKVTKAAGTKKQFQKF

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	0.07 RPM	79.81 RPM
SRP007412_cerebellum	0.22 RPM	69.13 RPM
SRP007412_heart	0.19 RPM	118.45 RPM
SRP007412_kidney	0.13 RPM	111.74 RPM
SRP007412_liver	0.08 RPM	98.26 RPM
SRP007412_testis	0.23 RPM	77.71 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3342 was not detected

EST

No EST(s) were mapped for retro_mmus_3342 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_151771	106 libraries	227 libraries	670 libraries	57 libraries	12 libraries

The graphical summary, for retro_mmus_3342 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_3342 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3342 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 100 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003631	9 retrocopies	retro_cfam_126, retro_cfam_1333, retro_cfam_1572, retro_cfam_1656, retro_cfam_1669, retro_cfam_1900, retro_cfam_1955, retro_cfam_2121, retro_cfam_248,
Danio rerio	ENSDARG00000053058	1 retrocopy	retro_drer_15,
Dipodomys ordii	ENSDORG00000012195	1 retrocopy	retro_dord_635,
Equus caballus	ENSECAG00000000370	1 retrocopy	retro_ecab_868,
Felis catus	ENSFCAG00000009196	13 retrocopies	retro_fcat_1362, retro_fcat_1491, retro_fcat_1535, retro_fcat_1564, retro_fcat_1719, retro_fcat_1945, retro_fcat_197, retro_fcat_1991, retro_fcat_273, retro_fcat_507, retro_fcat_792, retro_fcat_854, retro_fcat_995,
Microcebus murinus	ENSMICG00000002542	8 retrocopies	retro_mmur_1278, retro_mmur_1317, retro_mmur_186, retro_mmur_295, retro_mmur_430, retro_mmur_452, retro_mmur_812, retro_mmur_820,
Monodelphis domestica	ENSMODG00000013434	7 retrocopies	retro_mdom_1185, retro_mdom_1284, retro_mdom_1421, retro_mdom_1950, retro_mdom_636, retro_mdom_922, retro_mdom_978,
Mus musculus	ENSMUSG00000003429	16 retrocopies	retro_mmus_1738, retro_mmus_2230, retro_mmus_2255, retro_mmus_2322, retro_mmus_2486, retro_mmus_2854, retro_mmus_3048, retro_mmus_3051, retro_mmus_3060, retro_mmus_3342 , retro_mmus_398, retro_mmus_404, retro_mmus_714, retro_mmus_754, retro_mmus_842, retro_mmus_860,
Otolemur garnettii	ENSOGAG00000004627	7 retrocopies	retro_ogar_1290, retro_ogar_1813, retro_ogar_1910, retro_ogar_2037, retro_ogar_2573, retro_ogar_2640, retro_ogar_840,
Pan troglodytes	ENSPTRG00000011299	1 retrocopy	retro_ptro_88,
Rattus norvegicus	ENSRNOG00000020595	18 retrocopies	retro_rnor_1132, retro_rnor_1159, retro_rnor_1261, retro_rnor_1299, retro_rnor_1363, retro_rnor_1414, retro_rnor_1435, retro_rnor_1451, retro_rnor_1635, retro_rnor_1790, retro_rnor_2000, retro_rnor_2647, retro_rnor_385, retro_rnor_394, retro_rnor_538, retro_rnor_737, retro_rnor_835, retro_rnor_989,
Ictidomys tridecemlineatus	ENSSTOG00000023443	2 retrocopies	retro_itri_1033, retro_itri_805,
Tupaia belangeri	ENSTBEG00000016677	16 retrocopies	retro_tbel_125, retro_tbel_1361, retro_tbel_1753, retro_tbel_2071, retro_tbel_2207, retro_tbel_2808, retro_tbel_2947, retro_tbel_319, retro_tbel_3401, retro_tbel_3571, retro_tbel_3600, retro_tbel_3742, retro_tbel_449, retro_tbel_604, retro_tbel_801, retro_tbel_836,