RetrogeneDB ID: retro_mmus_115

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:107439214..107439562(-)
• Located in intron of: ENSMUSG00000031930

Retrocopy information

• Ensembl ID: ENSMUSG00000059775
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Rps26
• Ensembl ID: ENSMUSG00000025362
• Aliases: None
• Description: ribosomal protein S26 [Source:MGI Symbol;Acc:MGI:1351628]

Sequence

>retro_mmus_115
ATGACCAAAAAAAGAAGAAACAACGGTCGTGCCAAAAAGGGCCGCGGCCATGTGCAGCCCATTCGCTGCACGAACTGCGC
CCGGTGCGTGCCCAAGGATAAGGCCATCAAGAAGTTTGTCATTCGGAACATTGTAGAAGCCGCTGCTGTCAGGGACATAT
CTGAAGCAAGCGTCTTCGACGCCTACGTGCTTCCCAAGCTCTATGTCAAGCTGCATTATTGCGTGAGCTGTGCCATCCAT
AGCAAGGTTGTTAGGAATCGATCCCGCGAAGCCCGGAAGGACCGAACACCCCCACCACGATTCAGACCTGCTGGCGCTGC
ACCTCGACCTCCACCAAAGCCCATGTAA

Alignment

ORF - retro_mmus_115 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MTKKRRNNGRAKKGRGHVQPIRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDISEASVFDAYVLPKLYVK
          MTKKRRNNGRAKKGRGHVQPIRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDISEASVFDAYVLPKLYVK
Retrocopy MTKKRRNNGRAKKGRGHVQPIRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDISEASVFDAYVLPKLYVK

Parental  LHYCVSCAIHSKVVRNRSREARKDRTPPPRFRPAGAAPRPPPKPM
          LHYCVSCAIHSKVVRNRSREARKDRTPPPRFRPAGAAPRPPPKPM
Retrocopy LHYCVSCAIHSKVVRNRSREARKDRTPPPRFRPAGAAPRPPPKPM

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	0.09 RPM	38.92 RPM
SRP007412_cerebellum	0.17 RPM	25.58 RPM
SRP007412_heart	0.16 RPM	42.37 RPM
SRP007412_kidney	0.17 RPM	40.73 RPM
SRP007412_liver	0.30 RPM	49.16 RPM
SRP007412_testis	0.59 RPM	39.02 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_115 was not detected

EST

No EST(s) were mapped for retro_mmus_115 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_138760	25 libraries	11 libraries	247 libraries	372 libraries	417 libraries

The graphical summary, for retro_mmus_115 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_115 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_115 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 153 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003260	7 retrocopies	retro_amel_1037, retro_amel_1240, retro_amel_303, retro_amel_777, retro_amel_926, retro_amel_927, retro_amel_928,
Bos taurus	ENSBTAG00000038896	3 retrocopies	retro_btau_191, retro_btau_25, retro_btau_724,
Choloepus hoffmanni	ENSCHOG00000001489	10 retrocopies	retro_chof_1367, retro_chof_1423, retro_chof_1793, retro_chof_1825, retro_chof_2156, retro_chof_2255, retro_chof_2482, retro_chof_382, retro_chof_611, retro_chof_756,
Cavia porcellus	ENSCPOG00000023630	6 retrocopies	retro_cpor_115, retro_cpor_1231, retro_cpor_134, retro_cpor_173, retro_cpor_48, retro_cpor_992,
Dipodomys ordii	ENSDORG00000001151	2 retrocopies	retro_dord_239, retro_dord_279,
Echinops telfairi	ENSETEG00000004510	35 retrocopies	retro_etel_1072, retro_etel_1145, retro_etel_1149, retro_etel_1175, retro_etel_1321, retro_etel_1357, retro_etel_1407, retro_etel_1423, retro_etel_1469, retro_etel_1498, retro_etel_155, retro_etel_162, retro_etel_1647, retro_etel_1691, retro_etel_1703, retro_etel_1734, retro_etel_1801, retro_etel_181, retro_etel_1859, retro_etel_1913, retro_etel_1963, retro_etel_2006, retro_etel_2043, retro_etel_2138, retro_etel_2146, retro_etel_2175, retro_etel_269, retro_etel_354, retro_etel_38, retro_etel_424, retro_etel_462, retro_etel_741, retro_etel_77, retro_etel_894, retro_etel_898,
Felis catus	ENSFCAG00000013977	10 retrocopies	retro_fcat_1211, retro_fcat_1332, retro_fcat_1460, retro_fcat_1728, retro_fcat_1851, retro_fcat_1948, retro_fcat_1949, retro_fcat_428, retro_fcat_508, retro_fcat_949,
Gorilla gorilla	ENSGGOG00000011566	6 retrocopies	retro_ggor_106, retro_ggor_121, retro_ggor_19, retro_ggor_55, retro_ggor_56, retro_ggor_63,
Loxodonta africana	ENSLAFG00000013329	8 retrocopies	retro_lafr_180, retro_lafr_240, retro_lafr_40, retro_lafr_464, retro_lafr_513, retro_lafr_768, retro_lafr_835, retro_lafr_962,
Myotis lucifugus	ENSMLUG00000029968	10 retrocopies	retro_mluc_1153, retro_mluc_149, retro_mluc_1925, retro_mluc_2065, retro_mluc_2163, retro_mluc_2462, retro_mluc_266, retro_mluc_309, retro_mluc_332, retro_mluc_477,
Macaca mulatta	ENSMMUG00000017042	7 retrocopies	retro_mmul_1009, retro_mmul_1017, retro_mmul_1676, retro_mmul_1944, retro_mmul_2092, retro_mmul_294, retro_mmul_646,
Mus musculus	ENSMUSG00000025362	1 retrocopy	retro_mmus_115 ,
Pongo abelii	ENSPPYG00000004642	16 retrocopies	retro_pabe_1234, retro_pabe_1372, retro_pabe_140, retro_pabe_1405, retro_pabe_1431, retro_pabe_155, retro_pabe_1613, retro_pabe_237, retro_pabe_25, retro_pabe_2835, retro_pabe_3068, retro_pabe_3399, retro_pabe_3432, retro_pabe_809, retro_pabe_903, retro_pabe_924,
Pan troglodytes	ENSPTRG00000005075	1 retrocopy	retro_ptro_74,
Rattus norvegicus	ENSRNOG00000005517	1 retrocopy	retro_rnor_196,
Sus scrofa	ENSSSCG00000000374	2 retrocopies	retro_sscr_406, retro_sscr_650,
Ictidomys tridecemlineatus	ENSSTOG00000010559	12 retrocopies	retro_itri_1300, retro_itri_1446, retro_itri_1477, retro_itri_1488, retro_itri_289, retro_itri_418, retro_itri_469, retro_itri_470, retro_itri_643, retro_itri_652, retro_itri_729, retro_itri_871,
Tursiops truncatus	ENSTTRG00000015012	16 retrocopies	retro_ttru_1169, retro_ttru_1300, retro_ttru_131, retro_ttru_1319, retro_ttru_1329, retro_ttru_1412, retro_ttru_1514, retro_ttru_1635, retro_ttru_17, retro_ttru_1734, retro_ttru_1795, retro_ttru_1897, retro_ttru_428, retro_ttru_47, retro_ttru_651, retro_ttru_893,