RetrogeneDB ID: retro_mmus_1883

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:4700294..4700638(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083378
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rpl22
• Ensembl ID: ENSMUSG00000028936
• Aliases: Rpl22, 2700038K18Rik
• Description: ribosomal protein L22 [Source:MGI Symbol;Acc:MGI:99262]

Sequence

>retro_mmus_1883
AAGCAGGTTTTGAAGTGTACCCTGGACTGCACTCACCCTGTAGAAGATGGAATCATAGATGCTGCCAATTTTGAGCAGTT
CCTCCAGGAGAGAATCAAGGTGAATGGGAAAGCTGGCAATCTCGGCGGAGGAGTTGTGACCATCGAACAGAGCAAGAGCA
AGATCACTGTCACTTCGGAGGTGCCTTTCTCCAAAAGGTATTTGAAATATCTCACCAAAAAATATTTGAAGAAGAACAGC
CTCCGAGACTGGCTGCGTGTTGTCGCCAACAGCAAAGAGAGTTACGAGCTGCTTACGAGTTACTTCCAGATTAACCAGGA
TGAGAGGAGGACGAGGATTAGGAC

Alignment

ORF - retro_mmus_1883 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.38 %
• Parental protein coverage: 88.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KQVLKFTLDCTHPVEDGIMDAANFEQFLQERIKVNGKAGNLGGGVVTIERSKSKITVTSEVPFSKRYLKY
          KQVLK.TLDCTHPVEDGI.DAANFEQFLQERIKVNGKAGNLGGGVVTIE.SKSKITVTSEVPFSKRYLKY
Retrocopy KQVLKCTLDCTHPVEDGIIDAANFEQFLQERIKVNGKAGNLGGGVVTIEQSKSKITVTSEVPFSKRYLKY

Parental  LTKKYLKKNNLRDWLRVVANSKESYEL--RYFQINQDE-EEEEDED
          LTKKYLKKN.LRDWLRVVANSKESYEL...YFQINQDE.EE.ED.D
Retrocopy LTKKYLKKNSLRDWLRVVANSKESYELLTSYFQINQDE<EEDED*D

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	61.84 RPM
SRP007412_cerebellum	0.04 RPM	58.79 RPM
SRP007412_heart	0.03 RPM	91.62 RPM
SRP007412_kidney	0.13 RPM	115.17 RPM
SRP007412_liver	0.00 RPM	87.71 RPM
SRP007412_testis	0.09 RPM	47.84 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1883 was not detected

EST

No EST(s) were mapped for retro_mmus_1883 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_87324	475 libraries	509 libraries	86 libraries	2 libraries	0 libraries

The graphical summary, for retro_mmus_1883 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_1883 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1883 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 22 parental genes, and 187 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009864	7 retrocopies	retro_amel_1219, retro_amel_1247, retro_amel_1775, retro_amel_1793, retro_amel_369, retro_amel_830, retro_amel_870,
Bos taurus	ENSBTAG00000014423	4 retrocopies	retro_btau_1491, retro_btau_566, retro_btau_694, retro_btau_892,
Choloepus hoffmanni	ENSCHOG00000007477	2 retrocopies	retro_chof_1785, retro_chof_2537,
Callithrix jacchus	ENSCJAG00000000132	12 retrocopies	retro_cjac_1032, retro_cjac_1055, retro_cjac_1257, retro_cjac_1301, retro_cjac_2352, retro_cjac_2436, retro_cjac_2874, retro_cjac_2954, retro_cjac_3925, retro_cjac_472, retro_cjac_611, retro_cjac_867,
Dasypus novemcinctus	ENSDNOG00000013166	8 retrocopies	retro_dnov_1282, retro_dnov_1523, retro_dnov_2043, retro_dnov_2126, retro_dnov_38, retro_dnov_382, retro_dnov_425, retro_dnov_567,
Felis catus	ENSFCAG00000006320	3 retrocopies	retro_fcat_1591, retro_fcat_1656, retro_fcat_1715,
Homo sapiens	ENSG00000116251	16 retrocopies	retro_hsap_1162, retro_hsap_1299, retro_hsap_1445, retro_hsap_1720, retro_hsap_2136, retro_hsap_2138, retro_hsap_2142, retro_hsap_2306, retro_hsap_2315, retro_hsap_349, retro_hsap_3814, retro_hsap_485, retro_hsap_4865, retro_hsap_4909, retro_hsap_600, retro_hsap_726,
Gorilla gorilla	ENSGGOG00000027739	10 retrocopies	retro_ggor_1111, retro_ggor_1652, retro_ggor_1655, retro_ggor_1708, retro_ggor_1757, retro_ggor_2268, retro_ggor_2567, retro_ggor_37, retro_ggor_531, retro_ggor_613,
Loxodonta africana	ENSLAFG00000006352	5 retrocopies	retro_lafr_1100, retro_lafr_380, retro_lafr_649, retro_lafr_981, retro_lafr_993,
Macaca mulatta	ENSMMUG00000018347	12 retrocopies	retro_mmul_1004, retro_mmul_1044, retro_mmul_1047, retro_mmul_1512, retro_mmul_2209, retro_mmul_2264, retro_mmul_2467, retro_mmul_2601, retro_mmul_271, retro_mmul_445, retro_mmul_469, retro_mmul_80,
Mustela putorius furo	ENSMPUG00000007087	6 retrocopies	retro_mputfur_1074, retro_mputfur_1277, retro_mputfur_134, retro_mputfur_1433, retro_mputfur_578, retro_mputfur_873,
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	ENSNLEG00000010337	10 retrocopies	retro_nleu_1309, retro_nleu_2354, retro_nleu_2367, retro_nleu_2509, retro_nleu_2747, retro_nleu_2772, retro_nleu_2783, retro_nleu_2881, retro_nleu_2946, retro_nleu_3003,
Otolemur garnettii	ENSOGAG00000014776	7 retrocopies	retro_ogar_1116, retro_ogar_1415, retro_ogar_1418, retro_ogar_2188, retro_ogar_2979, retro_ogar_399, retro_ogar_917,
Pongo abelii	ENSPPYG00000001951	11 retrocopies	retro_pabe_1196, retro_pabe_1213, retro_pabe_1435, retro_pabe_166, retro_pabe_248, retro_pabe_3114, retro_pabe_349, retro_pabe_3782, retro_pabe_3817, retro_pabe_590, retro_pabe_966,
Pan troglodytes	ENSPTRG00000000076	14 retrocopies	retro_ptro_1562, retro_ptro_1563, retro_ptro_1630, retro_ptro_1690, retro_ptro_2596, retro_ptro_275, retro_ptro_3056, retro_ptro_3240, retro_ptro_365, retro_ptro_502, retro_ptro_517, retro_ptro_795, retro_ptro_950, retro_ptro_984,
Rattus norvegicus	ENSRNOG00000011104	5 retrocopies	retro_rnor_1315, retro_rnor_1687, retro_rnor_2089, retro_rnor_2149, retro_rnor_439,
Sus scrofa	ENSSSCG00000003367	4 retrocopies	retro_sscr_257, retro_sscr_276, retro_sscr_497, retro_sscr_509,
Tupaia belangeri	ENSTBEG00000009172	33 retrocopies	retro_tbel_1047, retro_tbel_1181, retro_tbel_1263, retro_tbel_1422, retro_tbel_1773, retro_tbel_1951, retro_tbel_2121, retro_tbel_2182, retro_tbel_2231, retro_tbel_2429, retro_tbel_2452, retro_tbel_2801, retro_tbel_2923, retro_tbel_3090, retro_tbel_3160, retro_tbel_3265, retro_tbel_3362, retro_tbel_3482, retro_tbel_3719, retro_tbel_3885, retro_tbel_3960, retro_tbel_397, retro_tbel_4199, retro_tbel_4225, retro_tbel_4386, retro_tbel_4437, retro_tbel_4607, retro_tbel_504, retro_tbel_582, retro_tbel_659, retro_tbel_680, retro_tbel_755, retro_tbel_920,
Tursiops truncatus	ENSTTRG00000010488	8 retrocopies	retro_ttru_1268, retro_ttru_147, retro_ttru_1519, retro_ttru_1564, retro_ttru_1739, retro_ttru_413, retro_ttru_714, retro_ttru_871,
Vicugna pacos	ENSVPAG00000009466	1 retrocopy	retro_vpac_330,