RetrogeneDB ID: retro_mmus_2984

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:3983789..3984187(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083344
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rps24
• Ensembl ID: ENSMUSG00000025290
• Aliases: None
• Description: ribosomal protein S24 [Source:MGI Symbol;Acc:MGI:98147]

Sequence

>retro_mmus_2984
ATGAATGACACAGTAACCATCCGGACCAGGAAGTTCATGACCAACCGTCTACTTCAGAGGAAACAGATGGTCATTGATGT
CCTTCATCCTGGGAAGGCAACAGCACCAAAAACAGATTTCAGGAAAAGCTGGCCAACATGTATAAAGATGCCACACCAGA
TGGCATCTTTGTATTTGGATTCAGAACCCACTTCGGTGGTGGCAAGACCACTGGCTTTGGCATGATCTATGATTCCTTAG
ATTATGCAAAGAAGAATGAGCCTAAACACAGACTTGCAAGACATGGCCTTTAGGAGAAGGAAAAGACCTCCCGAAAACAG
TGAAAGGAACGCAAGAACAGAATGAAGAAGGTCAGGGGCACGAAGGCCAATGTTGGTGCTGGCAAAAAGCCAAAGGAG

Alignment

ORF - retro_mmus_2984 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.11 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNDTVTIRTRKFMTNRLLQRKQMVIDVLHPGKATVPKTEIR-EKLAKMYK-TTPDVIFVFGFRTHFGGGK
          MNDTVTIRTRKFMTNRLLQRKQMVIDVLHPGKAT.PKT..R.EKLA.MYK..TPD.IFVFGFRTHFGGGK
Retrocopy MNDTVTIRTRKFMTNRLLQRKQMVIDVLHPGKATAPKTDFR<EKLANMYKDATPDGIFVFGFRTHFGGGK

Parental  TTGFGMIYDSLDYAKKNEPKHRLARHGLYEKKKTSRKQRKERKNRMKKVRGTAKANVGAGKKPKE
          TTGFGMIYDSLDYAKKNEPKHRLARHGL.EK.KTSRKQ.KERKNRMKKVRGT.KANVGAGKKPKE
Retrocopy TTGFGMIYDSLDYAKKNEPKHRLARHGL*EKEKTSRKQ*KERKNRMKKVRGT-KANVGAGKKPKE

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	95.09 RPM
SRP007412_cerebellum	0.00 RPM	56.45 RPM
SRP007412_heart	0.09 RPM	84.33 RPM
SRP007412_kidney	0.06 RPM	81.08 RPM
SRP007412_liver	0.03 RPM	94.84 RPM
SRP007412_testis	0.09 RPM	102.82 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2984 was not detected

EST

No EST(s) were mapped for retro_mmus_2984 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_134468	421 libraries	527 libraries	123 libraries	1 library	0 libraries

The graphical summary, for retro_mmus_2984 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_2984 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2984 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 71 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017818	17 retrocopies	retro_amel_1043, retro_amel_1258, retro_amel_1303, retro_amel_1397, retro_amel_145, retro_amel_1814, retro_amel_1832, retro_amel_225, retro_amel_24, retro_amel_251, retro_amel_328, retro_amel_331, retro_amel_515, retro_amel_718, retro_amel_768, retro_amel_81, retro_amel_886,
Cavia porcellus	ENSCPOG00000020096	3 retrocopies	retro_cpor_1333, retro_cpor_14, retro_cpor_923,
Dipodomys ordii	ENSDORG00000000189	4 retrocopies	retro_dord_248, retro_dord_498, retro_dord_717, retro_dord_766,
Felis catus	ENSFCAG00000000849	3 retrocopies	retro_fcat_19, retro_fcat_772, retro_fcat_85,
Gadus morhua	ENSGMOG00000012595	1 retrocopy	retro_gmor_15,
Loxodonta africana	ENSLAFG00000027878	10 retrocopies	retro_lafr_1017, retro_lafr_190, retro_lafr_303, retro_lafr_340, retro_lafr_439, retro_lafr_558, retro_lafr_596, retro_lafr_669, retro_lafr_854, retro_lafr_995,
Myotis lucifugus	ENSMLUG00000024102	1 retrocopy	retro_mluc_260,
Mustela putorius furo	ENSMPUG00000003778	1 retrocopy	retro_mputfur_10,
Mus musculus	ENSMUSG00000025290	13 retrocopies	retro_mmus_1101, retro_mmus_1462, retro_mmus_1589, retro_mmus_1592, retro_mmus_1599, retro_mmus_2134, retro_mmus_2332, retro_mmus_2497, retro_mmus_2984 , retro_mmus_3162, retro_mmus_321, retro_mmus_3233, retro_mmus_602,
Oryctolagus cuniculus	ENSOCUG00000012472	1 retrocopy	retro_ocun_16,
Otolemur garnettii	ENSOGAG00000011005	3 retrocopies	retro_ogar_1000, retro_ogar_2, retro_ogar_2130,
Pongo abelii	ENSPPYG00000002304	1 retrocopy	retro_pabe_184,
Rattus norvegicus	ENSRNOG00000010189	1 retrocopy	retro_rnor_206,
Sus scrofa	ENSSSCG00000010328	8 retrocopies	retro_sscr_1212, retro_sscr_14, retro_sscr_242, retro_sscr_289, retro_sscr_491, retro_sscr_564, retro_sscr_718, retro_sscr_902,
Ictidomys tridecemlineatus	ENSSTOG00000013000	4 retrocopies	retro_itri_167, retro_itri_376, retro_itri_528, retro_itri_728,