RetrogeneDB ID: retro_mmus_236

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:156366077..156366449(+)
• Located in intron of: ENSMUSG00000026601

Retrocopy information

• Ensembl ID: ENSMUSG00000078193
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Rpl35
• Ensembl ID: ENSMUSG00000062997
• Aliases: None
• Description: ribosomal protein L35 [Source:MGI Symbol;Acc:MGI:1913739]

Sequence

>retro_mmus_236
ATGGCCAAGATTAAGGCTCGGGACCTGCGCGGCAAGAAGAAGGAGGAGCTGTTGAAACAACTGGACGATCTGAAGGTGGA
ATTGTCCCAGCTTCGGGTCGCCAAAGTGACAGGCGGTGCCGCGTCCAAGCTCTCCAAGATACGAGTCGTTCGCAAGTCTA
TCGCCCGAGTCCTCACTGTTATTAACCAGACTCAAAAAGAAAACCTCAGGAAATTCTACAAGGGCAAGAAATACAAGCCC
CTAGACCTGCGACCCAAGAAGACTAGAGCCATGCGCCGCCGGCTCACCAAGCACGAGGAGAAGCTGAAGACCAAGAAGCA
GCAGCGGAAGGAGCGGCTGTATCCTCTGCGCAAGTATGCAGTCAAGGCCTGA

Alignment

ORF - retro_mmus_236 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  MAKIKARDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTVINQTQKENLR
          MAKIKARDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTVINQTQKENLR
Retrocopy MAKIKARDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTVINQTQKENLR

Parental  KFYKGKKYKPLDLRPKKTRAMRRRLTKHEEKLKTKKQQRKERLYPLRKYAVKA
          KFYKGKKYKPLDLRPKKTRAMRRRLTKHEEKLKTKKQQRKERLYPLRKYAVKA
Retrocopy KFYKGKKYKPLDLRPKKTRAMRRRLTKHEEKLKTKKQQRKERLYPLRKYAVKA

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	0.21 RPM	5.26 RPM
SRP007412_cerebellum	0.04 RPM	5.78 RPM
SRP007412_heart	0.22 RPM	13.51 RPM
SRP007412_kidney	0.10 RPM	11.78 RPM
SRP007412_liver	0.22 RPM	6.64 RPM
SRP007412_testis	0.32 RPM	12.26 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_236 was not detected

EST

No EST(s) were mapped for retro_mmus_236 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_70735	40 libraries	102 libraries	318 libraries	84 libraries	528 libraries

The graphical summary, for retro_mmus_236 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_236 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_236 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 29 parental genes, and 145 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016537	12 retrocopies	retro_amel_1010, retro_amel_1180, retro_amel_1341, retro_amel_1686, retro_amel_1746, retro_amel_1844, retro_amel_1887, retro_amel_351, retro_amel_584, retro_amel_819, retro_amel_893, retro_amel_94,
Bos taurus	ENSBTAG00000003205	3 retrocopies	retro_btau_1060, retro_btau_1340, retro_btau_185,
Canis familiaris	ENSCAFG00000020212	7 retrocopies	retro_cfam_1566, retro_cfam_1635, retro_cfam_2180, retro_cfam_294, retro_cfam_529, retro_cfam_738, retro_cfam_995,
Callithrix jacchus	ENSCJAG00000006724	5 retrocopies	retro_cjac_1074, retro_cjac_1308, retro_cjac_1377, retro_cjac_2458, retro_cjac_387,
Cavia porcellus	ENSCPOG00000022811	1 retrocopy	retro_cpor_414,
Equus caballus	ENSECAG00000009389	3 retrocopies	retro_ecab_1083, retro_ecab_115, retro_ecab_813,
Erinaceus europaeus	ENSEEUG00000012696	8 retrocopies	retro_eeur_144, retro_eeur_217, retro_eeur_225, retro_eeur_251, retro_eeur_319, retro_eeur_487, retro_eeur_533, retro_eeur_56,
Echinops telfairi	ENSETEG00000000876	10 retrocopies	retro_etel_1013, retro_etel_1267, retro_etel_1383, retro_etel_1556, retro_etel_1848, retro_etel_1931, retro_etel_303, retro_etel_637, retro_etel_747, retro_etel_942,
Felis catus	ENSFCAG00000030388	5 retrocopies	retro_fcat_1129, retro_fcat_1790, retro_fcat_1954, retro_fcat_397, retro_fcat_782,
Homo sapiens	ENSG00000136942	6 retrocopies	retro_hsap_1233, retro_hsap_326, retro_hsap_3579, retro_hsap_3832, retro_hsap_3867, retro_hsap_4026,
Gorilla gorilla	ENSGGOG00000004111	3 retrocopies	retro_ggor_2581, retro_ggor_351, retro_ggor_966,
Loxodonta africana	ENSLAFG00000010031	3 retrocopies	retro_lafr_128, retro_lafr_300, retro_lafr_642,
Microcebus murinus	ENSMICG00000002922	2 retrocopies	retro_mmur_1502, retro_mmur_215,
Myotis lucifugus	ENSMLUG00000029323	3 retrocopies	retro_mluc_1495, retro_mluc_2392, retro_mluc_969,
Macaca mulatta	ENSMMUG00000005260	5 retrocopies	retro_mmul_1304, retro_mmul_156, retro_mmul_1623, retro_mmul_1912, retro_mmul_265,
Monodelphis domestica	ENSMODG00000019753	1 retrocopy	retro_mdom_1039,
Mustela putorius furo	ENSMPUG00000013950	5 retrocopies	retro_mputfur_1136, retro_mputfur_1348, retro_mputfur_1478, retro_mputfur_1484, retro_mputfur_425,
Mus musculus	ENSMUSG00000062997	1 retrocopy	retro_mmus_236 ,
Nomascus leucogenys	ENSNLEG00000017303	7 retrocopies	retro_nleu_1153, retro_nleu_1770, retro_nleu_1850, retro_nleu_1921, retro_nleu_2104, retro_nleu_2836, retro_nleu_953,
Ornithorhynchus anatinus	ENSOANG00000011612	1 retrocopy	retro_oana_56,
Oryctolagus cuniculus	ENSOCUG00000002996	4 retrocopies	retro_ocun_200, retro_ocun_238, retro_ocun_451, retro_ocun_791,
Otolemur garnettii	ENSOGAG00000008513	7 retrocopies	retro_ogar_1265, retro_ogar_1271, retro_ogar_1828, retro_ogar_2005, retro_ogar_2253, retro_ogar_2610, retro_ogar_2903,
Ochotona princeps	ENSOPRG00000000406	9 retrocopies	retro_opri_1077, retro_opri_1134, retro_opri_244, retro_opri_273, retro_opri_339, retro_opri_473, retro_opri_565, retro_opri_628, retro_opri_650,
Pongo abelii	ENSPPYG00000019603	7 retrocopies	retro_pabe_1026, retro_pabe_165, retro_pabe_1718, retro_pabe_2948, retro_pabe_3064, retro_pabe_3303, retro_pabe_3304,
Pan troglodytes	ENSPTRG00000021361	6 retrocopies	retro_ptro_2426, retro_ptro_2609, retro_ptro_262, retro_ptro_2635, retro_ptro_2730, retro_ptro_846,
Rattus norvegicus	ENSRNOG00000014272	14 retrocopies	retro_rnor_1254, retro_rnor_126, retro_rnor_147, retro_rnor_1473, retro_rnor_1509, retro_rnor_1768, retro_rnor_1957, retro_rnor_205, retro_rnor_2183, retro_rnor_233, retro_rnor_2618, retro_rnor_2681, retro_rnor_2719, retro_rnor_451,
Sarcophilus harrisii	ENSSHAG00000004756	1 retrocopy	retro_shar_775,
Sus scrofa	ENSSSCG00000005595	5 retrocopies	retro_sscr_1168, retro_sscr_214, retro_sscr_553, retro_sscr_679, retro_sscr_905,
Ictidomys tridecemlineatus	ENSSTOG00000007901	1 retrocopy	retro_itri_1735,