RetrogeneDB ID: retro_mmus_2154

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:40780014..40780330(+)
• Located in intron of: ENSMUSG00000025757

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Rpl34
• Ensembl ID: ENSMUSG00000062006
• Aliases: Rpl34, 1100001I22Rik
• Description: ribosomal protein L34 [Source:MGI Symbol;Acc:MGI:1915686]

Sequence

>retro_mmus_2154
ATGGTCCAGCGTTTGACATACCATTGTATGCTTTCCTACAATACTGCTCTAACAAAACAAGGCTGTCTGGAACCCCTGGC
AACAGGATTGTTACCTTTACACCAAGAAGGTTGGGGAAGCACCTAAATCTGCATGTGGTGTGTGCCCATGCAGACTGTGA
GGGACTCGTGCCCGGAGACCCAAAGTCCTTAGGAGATTGTCTAAGACAAAGAAGTGTGTCAGCAGGGCCTGTGGTGGTTC
CATGTGTACCAAGTGTGTCCATGACAGGATCAAGCAGGCTTTCCTTATAGAGTAGCAGGAAAGTATTGACCGCATA

Alignment

ORF - retro_mmus_2154 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.85 %
• Parental protein coverage: 90.6 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVQRLTYRRRLSYNTA-SNKTRLSRTPGNRIV-YLYTKKVGKAPKSACGVCPGRLRGVRAVRPKVLMRLS
          MVQRLTY...LSYNTA.SNKTRLS.TPGNRIV.YLYTKKVG.APKSACGVCP.RL.G.RA.RPKVL.RLS
Retrocopy MVQRLTYHCMLSYNTA<SNKTRLSGTPGNRIV<YLYTKKVGEAPKSACGVCPCRL*GTRARRPKVLRRLS

Parental  KTQKHVSRAYGGSMCAKCVRDRIKRAFLIEEQKIVVKV
          KT.K.VSRA.GGSMC.KCV.DRIK.AFLIE.Q......
Retrocopy KTKKCVSRACGGSMCTKCVHDRIKQAFLIE*QESIDRI

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	41.14 RPM
SRP007412_cerebellum	0.04 RPM	24.40 RPM
SRP007412_heart	0.00 RPM	40.38 RPM
SRP007412_kidney	0.02 RPM	42.08 RPM
SRP007412_liver	0.03 RPM	45.41 RPM
SRP007412_testis	0.05 RPM	39.75 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2154 was not detected

EST

No EST(s) were mapped for retro_mmus_2154 retrocopy.

TSS

No TSS is located nearby retro_mmus_2154 retrocopy 5' end.

Lab

retro_mmus_2154 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2154 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 256 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009074	10 retrocopies	retro_chof_1313, retro_chof_1474, retro_chof_184, retro_chof_2249, retro_chof_2258, retro_chof_2260, retro_chof_2291, retro_chof_2411, retro_chof_281, retro_chof_324,
Callithrix jacchus	ENSCJAG00000015993	4 retrocopies	retro_cjac_130, retro_cjac_293, retro_cjac_83, retro_cjac_99,
Dasypus novemcinctus	ENSDNOG00000011179	26 retrocopies	retro_dnov_1172, retro_dnov_1775, retro_dnov_2020, retro_dnov_2025, retro_dnov_2079, retro_dnov_2127, retro_dnov_2137, retro_dnov_2275, retro_dnov_2385, retro_dnov_2501, retro_dnov_252, retro_dnov_262, retro_dnov_2627, retro_dnov_2651, retro_dnov_325, retro_dnov_339, retro_dnov_430, retro_dnov_553, retro_dnov_565, retro_dnov_59, retro_dnov_606, retro_dnov_635, retro_dnov_658, retro_dnov_862, retro_dnov_88, retro_dnov_978,
Echinops telfairi	ENSETEG00000003715	53 retrocopies	retro_etel_106, retro_etel_107, retro_etel_1125, retro_etel_1140, retro_etel_1182, retro_etel_1187, retro_etel_1232, retro_etel_124, retro_etel_1303, retro_etel_1324, retro_etel_145, retro_etel_1483, retro_etel_1515, retro_etel_1545, retro_etel_1547, retro_etel_158, retro_etel_170, retro_etel_1745, retro_etel_1767, retro_etel_179, retro_etel_1795, retro_etel_1890, retro_etel_1967, retro_etel_1973, retro_etel_2066, retro_etel_2094, retro_etel_217, retro_etel_2191, retro_etel_273, retro_etel_274, retro_etel_299, retro_etel_327, retro_etel_344, retro_etel_362, retro_etel_380, retro_etel_388, retro_etel_416, retro_etel_418, retro_etel_429, retro_etel_464, retro_etel_494, retro_etel_533, retro_etel_726, retro_etel_74, retro_etel_756, retro_etel_759, retro_etel_774, retro_etel_863, retro_etel_870, retro_etel_914, retro_etel_927, retro_etel_938, retro_etel_974,
Felis catus	ENSFCAG00000015502	16 retrocopies	retro_fcat_1240, retro_fcat_1334, retro_fcat_1401, retro_fcat_1453, retro_fcat_1492, retro_fcat_1508, retro_fcat_1619, retro_fcat_2010, retro_fcat_368, retro_fcat_434, retro_fcat_518, retro_fcat_544, retro_fcat_640, retro_fcat_941, retro_fcat_953, retro_fcat_956,
Gadus morhua	ENSGMOG00000009982	1 retrocopy	retro_gmor_31,
Loxodonta africana	ENSLAFG00000032615	6 retrocopies	retro_lafr_1039, retro_lafr_1232, retro_lafr_182, retro_lafr_298, retro_lafr_306, retro_lafr_733,
Macropus eugenii	ENSMEUG00000009361	3 retrocopies	retro_meug_1012, retro_meug_1754, retro_meug_1775,
Myotis lucifugus	ENSMLUG00000000464	4 retrocopies	retro_mluc_125, retro_mluc_1372, retro_mluc_1427, retro_mluc_1847,
Monodelphis domestica	ENSMODG00000020601	3 retrocopies	retro_mdom_1690, retro_mdom_774, retro_mdom_836,
Mus musculus	ENSMUSG00000062006	26 retrocopies	retro_mmus_1064, retro_mmus_1283, retro_mmus_1513, retro_mmus_1603, retro_mmus_1658, retro_mmus_2115, retro_mmus_2116, retro_mmus_215, retro_mmus_2154 , retro_mmus_2266, retro_mmus_2290, retro_mmus_2476, retro_mmus_2595, retro_mmus_2695, retro_mmus_2748, retro_mmus_2903, retro_mmus_2960, retro_mmus_3041, retro_mmus_3381, retro_mmus_3524, retro_mmus_467, retro_mmus_609, retro_mmus_640, retro_mmus_817, retro_mmus_823, retro_mmus_882,
Nomascus leucogenys	ENSNLEG00000012934	20 retrocopies	retro_nleu_1219, retro_nleu_1322, retro_nleu_1495, retro_nleu_150, retro_nleu_1617, retro_nleu_1703, retro_nleu_1839, retro_nleu_1915, retro_nleu_2101, retro_nleu_2260, retro_nleu_2268, retro_nleu_2575, retro_nleu_263, retro_nleu_2911, retro_nleu_2916, retro_nleu_2966, retro_nleu_3073, retro_nleu_38, retro_nleu_553, retro_nleu_861,
Ornithorhynchus anatinus	ENSOANG00000007856	1 retrocopy	retro_oana_92,
Ochotona princeps	ENSOPRG00000001780	11 retrocopies	retro_opri_1013, retro_opri_142, retro_opri_303, retro_opri_311, retro_opri_344, retro_opri_365, retro_opri_39, retro_opri_610, retro_opri_771, retro_opri_907, retro_opri_933,
Pelodiscus sinensis	ENSPSIG00000003295	1 retrocopy	retro_psin_60,
Rattus norvegicus	ENSRNOG00000016387	36 retrocopies	retro_rnor_1031, retro_rnor_1083, retro_rnor_1101, retro_rnor_1172, retro_rnor_1376, retro_rnor_1550, retro_rnor_1575, retro_rnor_1630, retro_rnor_1694, retro_rnor_1695, retro_rnor_1696, retro_rnor_1775, retro_rnor_1803, retro_rnor_1844, retro_rnor_1857, retro_rnor_2029, retro_rnor_2090, retro_rnor_2095, retro_rnor_2139, retro_rnor_2230, retro_rnor_2565, retro_rnor_2578, retro_rnor_2597, retro_rnor_2621, retro_rnor_2651, retro_rnor_2794, retro_rnor_282, retro_rnor_367, retro_rnor_500, retro_rnor_575, retro_rnor_605, retro_rnor_617, retro_rnor_672, retro_rnor_848, retro_rnor_866, retro_rnor_869,
Sarcophilus harrisii	ENSSHAG00000001357	1 retrocopy	retro_shar_799,
Sarcophilus harrisii	ENSSHAG00000002052	3 retrocopies	retro_shar_131, retro_shar_324, retro_shar_419,
Tupaia belangeri	ENSTBEG00000003574	24 retrocopies	retro_tbel_1109, retro_tbel_1298, retro_tbel_1337, retro_tbel_1532, retro_tbel_1781, retro_tbel_1857, retro_tbel_1941, retro_tbel_213, retro_tbel_2162, retro_tbel_2165, retro_tbel_2372, retro_tbel_2391, retro_tbel_2601, retro_tbel_279, retro_tbel_335, retro_tbel_3606, retro_tbel_3984, retro_tbel_4059, retro_tbel_4398, retro_tbel_657, retro_tbel_74, retro_tbel_901, retro_tbel_974, retro_tbel_983,
Tursiops truncatus	ENSTTRG00000003443	6 retrocopies	retro_ttru_1667, retro_ttru_1831, retro_ttru_355, retro_ttru_710, retro_ttru_717, retro_ttru_821,
Xenopus tropicalis	ENSXETG00000021095	1 retrocopy	retro_xtro_5,