RetrogeneDB ID: retro_mmus_2301

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:127691937..127692522(-)
• Located in intron of: ENSMUSG00000028028

Retrocopy information

• Ensembl ID: ENSMUSG00000089988
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rpl19
• Ensembl ID: ENSMUSG00000017404
• Aliases: None
• Description: ribosomal protein L19 [Source:MGI Symbol;Acc:MGI:98020]

Sequence

>retro_mmus_2301
ATGAGTATGCTCAGGCTACAGAAAAGGCTTGCCTCTAGTGTCCTCCGCTGTGGGAAAAAGAAGGTCTGGTTGGATCCCAA
TGAGACCAATGAAATCGCCAATGCCAACTTTCATCAGCAGATCAGGAAGCTGATCAAAGATGGGCTGATCATCCGCAAGC
CTGTGACTGTCCATTCCCGGGCTCATTGCCGGAAAAAAACCCTGGCCCGACGGAAGGGCAGGCATATGGGCATAGGGAAG
AGGGAGGGTACTGCCAATGCTCGGATGCCTGAGAAGGTGACCTGGATGAGAAGGATGAGGATCCTGCGCCAGCTTCTCAG
GAGATACCGGGAATCCAAGATTGACCGCCGTATGTATCACAGCCTGTACCTGAAGGTCAAAGGGAATGTGTTAAAAAACA
AGCGGATCCTCATGGAGCACATCCATAAACTGAAGGCGGACAAGGCCCACAAGAAGCTCCTGGCTGACCAGGCTGAGGCT
CGCAGGTCTAAGACCAAGGAAGCACGAAAGCGCCGGGAGGAGCACCTCCAGGCCAAGAAGGAAGAGATCATCAAGACTCT
GTCCAAGGAGGAGGAGACCAAGAAA

Alignment

ORF - retro_mmus_2301 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.39 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSMLRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVTVHSRARCRKNTLAR
          MSMLRLQKRLASSVLRCGKKKVWLDPNETNEIANAN..QQIRKLIKDGLIIRKPVTVHSRA.CRK.TLAR
Retrocopy MSMLRLQKRLASSVLRCGKKKVWLDPNETNEIANANFHQQIRKLIKDGLIIRKPVTVHSRAHCRKKTLAR

Parental  RKGRHMGIGKRKGTANARMPEKVTWMRRMRILRRLLRRYRESKKIDRHMYHSLYLKVKGNVFKNKRILME
          RKGRHMGIGKR.GTANARMPEKVTWMRRMRILR.LLRRYRES.KIDR.MYHSLYLKVKGNV.KNKRILME
Retrocopy RKGRHMGIGKREGTANARMPEKVTWMRRMRILRQLLRRYRES-KIDRRMYHSLYLKVKGNVLKNKRILME

Parental  HIHKLKADKARKKLLADQAEARRSKTKEARKRREERLQAKKEEIIKTLSKEEETKK
          HIHKLKADKA.KKLLADQAEARRSKTKEARKRREE.LQAKKEEIIKTLSKEEETKK
Retrocopy HIHKLKADKAHKKLLADQAEARRSKTKEARKRREEHLQAKKEEIIKTLSKEEETKK

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	0.14 RPM	54.16 RPM
SRP007412_cerebellum	0.26 RPM	33.22 RPM
SRP007412_heart	0.53 RPM	70.85 RPM
SRP007412_kidney	0.56 RPM	60.93 RPM
SRP007412_liver	0.19 RPM	55.27 RPM
SRP007412_testis	0.18 RPM	32.47 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2301 was not detected

EST

No EST(s) were mapped for retro_mmus_2301 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_92020	202 libraries	387 libraries	474 libraries	8 libraries	1 library

The graphical summary, for retro_mmus_2301 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_2301 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2301 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 163 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004121	5 retrocopies	retro_amel_1195, retro_amel_1663, retro_amel_451, retro_amel_531, retro_amel_889,
Callithrix jacchus	ENSCJAG00000008520	4 retrocopies	retro_cjac_131, retro_cjac_220, retro_cjac_32, retro_cjac_64,
Dasypus novemcinctus	ENSDNOG00000019742	7 retrocopies	retro_dnov_1478, retro_dnov_1897, retro_dnov_2, retro_dnov_2170, retro_dnov_2431, retro_dnov_691, retro_dnov_720,
Dipodomys ordii	ENSDORG00000004330	1 retrocopy	retro_dord_105,
Equus caballus	ENSECAG00000025080	6 retrocopies	retro_ecab_104, retro_ecab_319, retro_ecab_351, retro_ecab_456, retro_ecab_497, retro_ecab_905,
Homo sapiens	ENSG00000108298	21 retrocopies	retro_hsap_1085, retro_hsap_1802, retro_hsap_2072, retro_hsap_2157, retro_hsap_2209, retro_hsap_2406, retro_hsap_2651, retro_hsap_2679, retro_hsap_2850, retro_hsap_3012, retro_hsap_3155, retro_hsap_3274, retro_hsap_3401, retro_hsap_3885, retro_hsap_3933, retro_hsap_399, retro_hsap_3991, retro_hsap_4219, retro_hsap_4680, retro_hsap_4774, retro_hsap_739,
Macaca mulatta	ENSMMUG00000004235	2 retrocopies	retro_mmul_283, retro_mmul_63,
Mus musculus	ENSMUSG00000017404	25 retrocopies	retro_mmus_1174, retro_mmus_1235, retro_mmus_1248, retro_mmus_1273, retro_mmus_1323, retro_mmus_1397, retro_mmus_1591, retro_mmus_1614, retro_mmus_1699, retro_mmus_1700, retro_mmus_1877, retro_mmus_1885, retro_mmus_1964, retro_mmus_2301 , retro_mmus_2688, retro_mmus_2749, retro_mmus_2967, retro_mmus_3110, retro_mmus_3187, retro_mmus_3310, retro_mmus_341, retro_mmus_3413, retro_mmus_507, retro_mmus_571, retro_mmus_600,
Nomascus leucogenys	ENSNLEG00000000748	19 retrocopies	retro_nleu_1182, retro_nleu_1570, retro_nleu_1602, retro_nleu_1620, retro_nleu_1889, retro_nleu_2171, retro_nleu_2236, retro_nleu_2284, retro_nleu_2335, retro_nleu_2430, retro_nleu_2446, retro_nleu_2538, retro_nleu_2695, retro_nleu_2702, retro_nleu_2735, retro_nleu_3116, retro_nleu_479, retro_nleu_540, retro_nleu_656,
Pongo abelii	ENSPPYG00000008492	20 retrocopies	retro_pabe_1546, retro_pabe_1687, retro_pabe_1709, retro_pabe_1815, retro_pabe_2177, retro_pabe_2300, retro_pabe_2320, retro_pabe_2496, retro_pabe_2625, retro_pabe_2799, retro_pabe_2800, retro_pabe_3166, retro_pabe_3278, retro_pabe_3299, retro_pabe_3513, retro_pabe_3635, retro_pabe_3829, retro_pabe_4, retro_pabe_973, retro_pabe_980,
Pteropus vampyrus	ENSPVAG00000008498	9 retrocopies	retro_pvam_1191, retro_pvam_1332, retro_pvam_183, retro_pvam_244, retro_pvam_468, retro_pvam_792, retro_pvam_914, retro_pvam_918, retro_pvam_950,
Rattus norvegicus	ENSRNOG00000004741	37 retrocopies	retro_rnor_1029, retro_rnor_1039, retro_rnor_1295, retro_rnor_1338, retro_rnor_1405, retro_rnor_1440, retro_rnor_1449, retro_rnor_1478, retro_rnor_1512, retro_rnor_1525, retro_rnor_1558, retro_rnor_1577, retro_rnor_1765, retro_rnor_1766, retro_rnor_1795, retro_rnor_1814, retro_rnor_1860, retro_rnor_1885, retro_rnor_1905, retro_rnor_1907, retro_rnor_1970, retro_rnor_1981, retro_rnor_208, retro_rnor_2169, retro_rnor_2522, retro_rnor_2536, retro_rnor_2708, retro_rnor_2773, retro_rnor_2783, retro_rnor_2921, retro_rnor_2943, retro_rnor_326, retro_rnor_426, retro_rnor_434, retro_rnor_464, retro_rnor_465, retro_rnor_829,
Sarcophilus harrisii	ENSSHAG00000016482	4 retrocopies	retro_shar_159, retro_shar_287, retro_shar_317, retro_shar_415,
Sus scrofa	ENSSSCG00000017509	3 retrocopies	retro_sscr_1108, retro_sscr_398, retro_sscr_913,