RetrogeneDB ID: retro_mmus_5

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:95622277..95622775(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000060438
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Rps10
• Ensembl ID: ENSMUSG00000052146
• Aliases: Rps10, 2210402A09Rik
• Description: ribosomal protein S10 [Source:MGI Symbol;Acc:MGI:1914347]

Sequence

>retro_mmus_5
ATGTTGATGCCTAAGAAGAATCGGATTGCCATCTACGAACTCCTTTTTAAGGAGGGCGTGATGGTCGCCAAAAAGGATGT
CCACATGCCTAAGCACCCCGAGCTGGCAGACAAAAATGTGCCCAACCTTCATGTAATGAAGGCCATGCAGTCTCTCAAGT
CTCGAGGCTACGTGAAGGAACAGTTTGCTTGGAGACATTTCTACTGGTACCTTACGAACGAGGGCATCCAGTGTCCCCGA
GACTACCTGCACCTACCCCCGGAGATCGTGCCCGCCACCCTGCGCCGCAGCCGTCCCGAGACCGGCAGGCCTCGGCCCAA
AGGTCCAGAGGGTGAGCGACCTGCAAGATTCACAAGAGGGGAGGCTGACAGAGACACCTACAGAAGGAGCGCTGTGCCCC
CTGGAGCTGACAAGAAAACTGAGGCTGGGGCTGGCTCGGCCACTGAGTTCCAGTTTAGAGGCGGCTTTGGTCGTGGACGT
GGTCAGCCACCTCAGTGA

Alignment

ORF - retro_mmus_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.18 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKEQFAWRHFYWY
          MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKEQFAWRHFYWY
Retrocopy MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKEQFAWRHFYWY

Parental  LTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGPEGERPARFTRGEADRDTYRRSAVPPGADKKA
          LTNEGIQ..RDYLHLPPEIVPATLRRSRPETGRPRPKGPEGERPARFTRGEADRDTYRRSAVPPGADKK.
Retrocopy LTNEGIQCPRDYLHLPPEIVPATLRRSRPETGRPRPKGPEGERPARFTRGEADRDTYRRSAVPPGADKKT

Parental  EAGAGSATEFQFRGGFGRGRGQPPQ
          EAGAGSATEFQFRGGFGRGRGQPPQ
Retrocopy EAGAGSATEFQFRGGFGRGRGQPPQ

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	28.50 RPM
SRP007412_cerebellum	0.00 RPM	20.41 RPM
SRP007412_heart	0.28 RPM	54.48 RPM
SRP007412_kidney	0.12 RPM	36.63 RPM
SRP007412_liver	0.00 RPM	39.08 RPM
SRP007412_testis	0.18 RPM	18.20 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_5 was not detected

EST

No EST(s) were mapped for retro_mmus_5 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_97937	38 libraries	94 libraries	280 libraries	5 libraries	655 libraries

The graphical summary, for retro_mmus_5 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_5 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_5 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 26 parental genes, and 154 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001047	4 retrocopies	retro_amel_1408, retro_amel_1706, retro_amel_446, retro_amel_890,
Canis familiaris	ENSCAFG00000001214	2 retrocopies	retro_cfam_1, retro_cfam_92,
Callithrix jacchus	ENSCJAG00000015250	4 retrocopies	retro_cjac_215, retro_cjac_296, retro_cjac_325, retro_cjac_63,
Cavia porcellus	ENSCPOG00000008613	2 retrocopies	retro_cpor_1245, retro_cpor_345,
Dasypus novemcinctus	ENSDNOG00000011670	2 retrocopies	retro_dnov_2303, retro_dnov_2558,
Dipodomys ordii	ENSDORG00000012060	6 retrocopies	retro_dord_225, retro_dord_494, retro_dord_641, retro_dord_73, retro_dord_74, retro_dord_767,
Equus caballus	ENSECAG00000006430	1 retrocopy	retro_ecab_198,
Felis catus	ENSFCAG00000015355	3 retrocopies	retro_fcat_1443, retro_fcat_1681, retro_fcat_1757,
Homo sapiens	ENSG00000124614	24 retrocopies	retro_hsap_1509, retro_hsap_1628, retro_hsap_1630, retro_hsap_1657, retro_hsap_1923, retro_hsap_2003, retro_hsap_2113, retro_hsap_229, retro_hsap_2415, retro_hsap_2573, retro_hsap_2574, retro_hsap_2830, retro_hsap_289, retro_hsap_3007, retro_hsap_3170, retro_hsap_3243, retro_hsap_3436, retro_hsap_3454, retro_hsap_3720, retro_hsap_4114, retro_hsap_4190, retro_hsap_460, retro_hsap_869, retro_hsap_992,
Latimeria chalumnae	ENSLACG00000017219	1 retrocopy	retro_lcha_26,
Loxodonta africana	ENSLAFG00000008539	1 retrocopy	retro_lafr_756,
Macaca mulatta	ENSMMUG00000000267	2 retrocopies	retro_mmul_332, retro_mmul_555,
Monodelphis domestica	ENSMODG00000013929	2 retrocopies	retro_mdom_1889, retro_mdom_437,
Mustela putorius furo	ENSMPUG00000003117	3 retrocopies	retro_mputfur_1347, retro_mputfur_1533, retro_mputfur_1579,
Mus musculus	ENSMUSG00000052146	9 retrocopies	retro_mmus_1376, retro_mmus_1500, retro_mmus_1831, retro_mmus_2431, retro_mmus_2551, retro_mmus_2708, retro_mmus_3651, retro_mmus_5 , retro_mmus_858,
Nomascus leucogenys	ENSNLEG00000008336	24 retrocopies	retro_nleu_1064, retro_nleu_1206, retro_nleu_1217, retro_nleu_1366, retro_nleu_1463, retro_nleu_1496, retro_nleu_165, retro_nleu_1694, retro_nleu_1748, retro_nleu_1969, retro_nleu_2120, retro_nleu_2452, retro_nleu_2678, retro_nleu_2791, retro_nleu_2833, retro_nleu_2834, retro_nleu_2950, retro_nleu_2955, retro_nleu_3021, retro_nleu_3047, retro_nleu_3052, retro_nleu_579, retro_nleu_850, retro_nleu_882,
Oryctolagus cuniculus	ENSOCUG00000011373	2 retrocopies	retro_ocun_250, retro_ocun_874,
Otolemur garnettii	ENSOGAG00000001365	5 retrocopies	retro_ogar_2166, retro_ogar_2314, retro_ogar_2553, retro_ogar_415, retro_ogar_873,
Ochotona princeps	ENSOPRG00000002693	2 retrocopies	retro_opri_297, retro_opri_800,
Procavia capensis	ENSPCAG00000012795	1 retrocopy	retro_pcap_309,
Pongo abelii	ENSPPYG00000016516	2 retrocopies	retro_pabe_2319, retro_pabe_97,
Pan troglodytes	ENSPTRG00000018063	26 retrocopies	retro_ptro_1021, retro_ptro_1090, retro_ptro_1092, retro_ptro_1126, retro_ptro_1160, retro_ptro_1287, retro_ptro_1335, retro_ptro_1391, retro_ptro_1497, retro_ptro_1502, retro_ptro_1503, retro_ptro_1788, retro_ptro_1918, retro_ptro_199, retro_ptro_2192, retro_ptro_2330, retro_ptro_2342, retro_ptro_238, retro_ptro_2519, retro_ptro_2793, retro_ptro_2797, retro_ptro_2919, retro_ptro_3051, retro_ptro_3078, retro_ptro_347, retro_ptro_603,
Sarcophilus harrisii	ENSSHAG00000000731	3 retrocopies	retro_shar_243, retro_shar_334, retro_shar_724,
Ictidomys tridecemlineatus	ENSSTOG00000013486	5 retrocopies	retro_itri_1448, retro_itri_1515, retro_itri_230, retro_itri_787, retro_itri_963,
Tupaia belangeri	ENSTBEG00000001492	16 retrocopies	retro_tbel_1302, retro_tbel_175, retro_tbel_1775, retro_tbel_2039, retro_tbel_2061, retro_tbel_2062, retro_tbel_2766, retro_tbel_2814, retro_tbel_314, retro_tbel_3359, retro_tbel_483, retro_tbel_522, retro_tbel_667, retro_tbel_980, retro_tbel_981, retro_tbel_986,
Tursiops truncatus	ENSTTRG00000015064	2 retrocopies	retro_ttru_1089, retro_ttru_1211,