RetrogeneDB ID: retro_mmus_3500

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:103507254..103507584(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082383
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rpl13
• Ensembl ID: ENSMUSG00000000740
• Aliases: Rpl13, A52, L13
• Description: ribosomal protein L13 [Source:MGI Symbol;Acc:MGI:105922]

Sequence

>retro_mmus_3500
ACCATCGGCATCTCTGTGGACCCAAGGAGGCGAAACAAATCCACTGAATCGCTGCAAGCTACCATGCAGCGCCTAAAGGA
GTACTGCTCAAAGCTCATACTTTCCCCCAGGAAGCCTTCTCTGAAGAAGGGAGACAGTTCTGTTGAAGAACTTAAATTGG
CCACCCAACTGACAGGACCTGTGATGCCCACCCGGAATGTGTACAAAAAGGAAAAGGCCAGCGTCGACACAGAAGAGAAC
TCTAAGGCTTTTGCCAGTCTTCACATGGCCTGTGCCAATGCCCAAGCAAAAAGCGTGAAGGAAGCTGCGGAGCAAGATGT
TGAAGAGAAA

Alignment

ORF - retro_mmus_3500 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.45 %
• Parental protein coverage: 53.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TIGISVDPRRRNKSTESLQANVQRLKEYRSKLILFPRKPSAPKKGDSSAEELKLATQLTGPVMPIRNVYK
          TIGISVDPRRRNKSTESLQA..QRLKEY.SKLIL.PRKPS..KKGDSS.EELKLATQLTGPVMP.RNVYK
Retrocopy TIGISVDPRRRNKSTESLQATMQRLKEYCSKLILSPRKPSL-KKGDSSVEELKLATQLTGPVMPTRNVYK

Parental  KEKARVITEEEKNFKAFASLRMARANARLFGIRAKRAKEAAEQ
          KEKA.V.TEE..N.KAFASL.MA.ANA..............E.
Retrocopy KEKASVDTEE--NSKAFASLHMACANAQAKSVKEAAEQDVEEK

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	0.56 RPM	36.87 RPM
SRP007412_cerebellum	0.30 RPM	16.93 RPM
SRP007412_heart	0.22 RPM	41.50 RPM
SRP007412_kidney	0.33 RPM	25.02 RPM
SRP007412_liver	0.49 RPM	22.80 RPM
SRP007412_testis	0.00 RPM	37.64 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3500 was not detected

EST

No EST(s) were mapped for retro_mmus_3500 retrocopy.

TSS

No TSS is located nearby retro_mmus_3500 retrocopy 5' end.

Lab

retro_mmus_3500 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3500 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 24 parental genes, and 153 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017072	1 retrocopy	retro_acar_70,
Ailuropoda melanoleuca	ENSAMEG00000001111	5 retrocopies	retro_amel_1268, retro_amel_1319, retro_amel_188, retro_amel_411, retro_amel_802,
Bos taurus	ENSBTAG00000012044	2 retrocopies	retro_btau_716, retro_btau_817,
Canis familiaris	ENSCAFG00000019840	5 retrocopies	retro_cfam_1135, retro_cfam_1919, retro_cfam_2122, retro_cfam_565, retro_cfam_897,
Callithrix jacchus	ENSCJAG00000009672	5 retrocopies	retro_cjac_2607, retro_cjac_2961, retro_cjac_4054, retro_cjac_663, retro_cjac_747,
Cavia porcellus	ENSCPOG00000027348	4 retrocopies	retro_cpor_1014, retro_cpor_1192, retro_cpor_1242, retro_cpor_491,
Echinops telfairi	ENSETEG00000015057	4 retrocopies	retro_etel_1240, retro_etel_1382, retro_etel_1606, retro_etel_703,
Felis catus	ENSFCAG00000003338	4 retrocopies	retro_fcat_1946, retro_fcat_706, retro_fcat_852, retro_fcat_866,
Homo sapiens	ENSG00000167526	12 retrocopies	retro_hsap_1377, retro_hsap_1810, retro_hsap_2070, retro_hsap_2430, retro_hsap_2485, retro_hsap_2824, retro_hsap_3207, retro_hsap_3281, retro_hsap_3443, retro_hsap_4074, retro_hsap_478, retro_hsap_951,
Gorilla gorilla	ENSGGOG00000025427	6 retrocopies	retro_ggor_1548, retro_ggor_1963, retro_ggor_2231, retro_ggor_2732, retro_ggor_562, retro_ggor_767,
Loxodonta africana	ENSLAFG00000004054	5 retrocopies	retro_lafr_659, retro_lafr_766, retro_lafr_827, retro_lafr_828, retro_lafr_829,
Microcebus murinus	ENSMICG00000008191	4 retrocopies	retro_mmur_249, retro_mmur_288, retro_mmur_779, retro_mmur_908,
Myotis lucifugus	ENSMLUG00000010950	6 retrocopies	retro_mluc_1431, retro_mluc_1436, retro_mluc_1549, retro_mluc_2022, retro_mluc_891, retro_mluc_991,
Macaca mulatta	ENSMMUG00000017928	7 retrocopies	retro_mmul_2021, retro_mmul_2150, retro_mmul_2350, retro_mmul_579, retro_mmul_593, retro_mmul_737, retro_mmul_781,
Monodelphis domestica	ENSMODG00000003663	4 retrocopies	retro_mdom_1001, retro_mdom_416, retro_mdom_439, retro_mdom_674,
Mus musculus	ENSMUSG00000000740	23 retrocopies	retro_mmus_1091, retro_mmus_1522, retro_mmus_1533, retro_mmus_1854, retro_mmus_2074, retro_mmus_2163, retro_mmus_2186, retro_mmus_2321, retro_mmus_2333, retro_mmus_2351, retro_mmus_25, retro_mmus_2668, retro_mmus_2718, retro_mmus_3097, retro_mmus_3274, retro_mmus_3453, retro_mmus_3489, retro_mmus_3500 , retro_mmus_355, retro_mmus_3711, retro_mmus_692, retro_mmus_732, retro_mmus_863,
Nomascus leucogenys	ENSNLEG00000015774	13 retrocopies	retro_nleu_1156, retro_nleu_1202, retro_nleu_2299, retro_nleu_238, retro_nleu_2457, retro_nleu_2530, retro_nleu_2657, retro_nleu_273, retro_nleu_2732, retro_nleu_2885, retro_nleu_3016, retro_nleu_789, retro_nleu_892,
Ornithorhynchus anatinus	ENSOANG00000006729	1 retrocopy	retro_oana_78,
Otolemur garnettii	ENSOGAG00000026444	3 retrocopies	retro_ogar_1165, retro_ogar_1831, retro_ogar_1853,
Pan troglodytes	ENSPTRG00000008480	12 retrocopies	retro_ptro_1175, retro_ptro_1382, retro_ptro_1402, retro_ptro_1438, retro_ptro_1914, retro_ptro_2219, retro_ptro_2242, retro_ptro_2336, retro_ptro_2761, retro_ptro_359, retro_ptro_658, retro_ptro_946,
Pteropus vampyrus	ENSPVAG00000015130	6 retrocopies	retro_pvam_1174, retro_pvam_1289, retro_pvam_1344, retro_pvam_228, retro_pvam_58, retro_pvam_616,
Rattus norvegicus	ENSRNOG00000015335	14 retrocopies	retro_rnor_1054, retro_rnor_1260, retro_rnor_158, retro_rnor_160, retro_rnor_1719, retro_rnor_1720, retro_rnor_1834, retro_rnor_1848, retro_rnor_2471, retro_rnor_2574, retro_rnor_2608, retro_rnor_2787, retro_rnor_2854, retro_rnor_682,
Sus scrofa	ENSSSCG00000024974	3 retrocopies	retro_sscr_1044, retro_sscr_725, retro_sscr_884,
Vicugna pacos	ENSVPAG00000000569	4 retrocopies	retro_vpac_310, retro_vpac_312, retro_vpac_576, retro_vpac_631,