RetrogeneDB ID: retro_mmus_2633

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:22528323..22528689(-)
• Located in intron of: ENSMUSG00000029012

Retrocopy information

• Ensembl ID: ENSMUSG00000084235
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rpl22l1
• Ensembl ID: ENSMUSG00000039221
• Aliases: Rpl22l1, 3110001N18Rik, AU041196
• Description: ribosomal protein L22 like 1 [Source:MGI Symbol;Acc:MGI:1915278]

Sequence

>retro_mmus_2633
ATGGCGCCGCAGAAAGACAAGAAGCCTAAGAAGTCCACCTGGAGGTTTCATTTGGACCTTACTCATCCAGTAGAAGATGG
AATTTTTGACTCTGGAAATTTTGAACAGTTTCTACGGGAGAAGGTTAAAGTCAATGGGAAAACTGGAAATCTTGGCAATG
TTGTTCACATTGAACGCCTGAAGAATAAAATCACAGTTGTTTCTGAGAAACAGTTCTCCAAAAGGTATTTGAAATATCTT
ACCAAGAAATACCTTAAGAAGAATAATCTCCGTGATTGGCTACGTGTGGTCGCATCTGACAAGGAGACTTACGAACTTCG
TTATTTCCAGATTAGTCAAGATGAAGATGGTTCAGAGCCTGAGGAC

Alignment

ORF - retro_mmus_2633 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.18 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPQKDKKPKKSTWRFHLDLTHPVEDGIFDSGNFEQFLREKVKVNGKTGNLGNVVHIERLKNKITVVSEK
          MAPQKDKKPKKSTWRFHLDLTHPVEDGIFDSGNFEQFLREKVKVNGKTGNLGNVVHIERLKNKITVVSEK
Retrocopy MAPQKDKKPKKSTWRFHLDLTHPVEDGIFDSGNFEQFLREKVKVNGKTGNLGNVVHIERLKNKITVVSEK

Parental  QFSKRYLKYLTKKYLKKNNLRDWLRVVASDKETYELRYFQISQDEDGSESED
          QFSKRYLKYLTKKYLKKNNLRDWLRVVASDKETYELRYFQISQDEDGSE.ED
Retrocopy QFSKRYLKYLTKKYLKKNNLRDWLRVVASDKETYELRYFQISQDEDGSEPED

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	0.12 RPM	17.36 RPM
SRP007412_cerebellum	0.04 RPM	5.17 RPM
SRP007412_heart	0.12 RPM	5.35 RPM
SRP007412_kidney	0.12 RPM	6.78 RPM
SRP007412_liver	0.03 RPM	7.46 RPM
SRP007412_testis	0.05 RPM	7.27 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2633 was not detected

EST

No EST(s) were mapped for retro_mmus_2633 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_112675	14 libraries	3 libraries	23 libraries	86 libraries	946 libraries

The graphical summary, for retro_mmus_2633 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_2633 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2633 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 28 parental genes, and 86 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004730	1 retrocopy	retro_amel_7,
Canis familiaris	ENSCAFG00000014955	2 retrocopies	retro_cfam_1410, retro_cfam_773,
Callithrix jacchus	ENSCJAG00000002427	1 retrocopy	retro_cjac_3983,
Cavia porcellus	ENSCPOG00000009215	1 retrocopy	retro_cpor_1544,
Equus caballus	ENSECAG00000018894	1 retrocopy	retro_ecab_728,
Erinaceus europaeus	ENSEEUG00000011941	5 retrocopies	retro_eeur_436, retro_eeur_60, retro_eeur_602, retro_eeur_676, retro_eeur_691,
Echinops telfairi	ENSETEG00000010658	9 retrocopies	retro_etel_1289, retro_etel_1433, retro_etel_1459, retro_etel_151, retro_etel_1680, retro_etel_335, retro_etel_513, retro_etel_800, retro_etel_936,
Homo sapiens	ENSG00000163584	1 retrocopy	retro_hsap_2929,
Gorilla gorilla	ENSGGOG00000001734	1 retrocopy	retro_ggor_2031,
Gadus morhua	ENSGMOG00000004077	1 retrocopy	retro_gmor_10,
Loxodonta africana	ENSLAFG00000013220	2 retrocopies	retro_lafr_1121, retro_lafr_682,
Macropus eugenii	ENSMEUG00000009484	1 retrocopy	retro_meug_390,
Myotis lucifugus	ENSMLUG00000023052	2 retrocopies	retro_mluc_1183, retro_mluc_1588,
Myotis lucifugus	ENSMLUG00000027683	8 retrocopies	retro_mluc_1225, retro_mluc_1403, retro_mluc_1690, retro_mluc_1804, retro_mluc_1967, retro_mluc_2383, retro_mluc_2401, retro_mluc_668,
Macaca mulatta	ENSMMUG00000022881	2 retrocopies	retro_mmul_1927, retro_mmul_1954,
Mus musculus	ENSMUSG00000028936	5 retrocopies	retro_mmus_1883, retro_mmus_1906, retro_mmus_2123, retro_mmus_2459, retro_mmus_3171,
Mus musculus	ENSMUSG00000039221	4 retrocopies	retro_mmus_1380, retro_mmus_2633 , retro_mmus_2674, retro_mmus_3631,
Nomascus leucogenys	ENSNLEG00000005287	2 retrocopies	retro_nleu_1918, retro_nleu_2266,
Oryctolagus cuniculus	ENSOCUG00000014962	2 retrocopies	retro_ocun_1, retro_ocun_256,
Otolemur garnettii	ENSOGAG00000012642	2 retrocopies	retro_ogar_1434, retro_ogar_780,
Procavia capensis	ENSPCAG00000008704	1 retrocopy	retro_pcap_105,
Pongo abelii	ENSPPYG00000025900	1 retrocopy	retro_pabe_2524,
Pteropus vampyrus	ENSPVAG00000011524	1 retrocopy	retro_pvam_328,
Rattus norvegicus	ENSRNOG00000011817	2 retrocopies	retro_rnor_111, retro_rnor_2152,
Sus scrofa	ENSSSCG00000027441	5 retrocopies	retro_sscr_1039, retro_sscr_129, retro_sscr_141, retro_sscr_85, retro_sscr_860,
Ictidomys tridecemlineatus	ENSSTOG00000022972	3 retrocopies	retro_itri_1511, retro_itri_1533, retro_itri_492,
Tupaia belangeri	ENSTBEG00000000357	17 retrocopies	retro_tbel_1135, retro_tbel_1188, retro_tbel_2011, retro_tbel_2073, retro_tbel_2081, retro_tbel_226, retro_tbel_2325, retro_tbel_2333, retro_tbel_2434, retro_tbel_2936, retro_tbel_3526, retro_tbel_3796, retro_tbel_4070, retro_tbel_4372, retro_tbel_4573, retro_tbel_4681, retro_tbel_575,
Tursiops truncatus	ENSTTRG00000007035	3 retrocopies	retro_ttru_1180, retro_ttru_168, retro_ttru_968,