RetrogeneDB ID: retro_rnor_2690

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:61252224..61252757(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000013487
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rpl11
• Ensembl ID: ENSRNOG00000026260
• Aliases: None
• Description: 60S ribosomal protein L11 [Source:UniProtKB/Swiss-Prot;Acc:P62914]

Sequence

>retro_rnor_2690
ATGGCGCAAGATCAGGGTGAAAAGGAGAACCCCATGCGGGAACTTCGTATCCGAAAGCTCTGCCTCAATATCTTCGTGGG
GAAGAGTGGAGACAGACTGACCCAAGCAGCCAAGGTGTTGGAGCAGCTCACAGGCCAGACCCCTGTGTTTTCCAAAGCTA
GATACATCGTCAGGTCCTTTGCATCCGGAGAAATGAGAAAATCGCTGTTCACTGCACTGTCCATGGAGCCAAGGCAGAGG
AGATTCTGGAGAAAGGCCTGAAGGTGCGAGAGTACGAATTACGGAAGAATAACTTCTCAGATACCAGCAACTTTGGCTTT
GGGATTCAGGAACACATTGACCTGGGCATCAAATATGACCTAAGCGTTGGCATCTATGGCCTGGATTTCTATGTGGTGCT
GGGTAGGCCAGGTTTCAGCATCGCAGACAAGAAGCGCAGAACAGGCTTCATTGGGGTCAAACGCAGAATCAGCAAAGAGG
AGGCCATGCGCTGGTTCCAGCAGAAGTATGATGGCATCATCCTTCCTGGCAAA

Alignment

ORF - retro_rnor_2690 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.74 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAQDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSFG-IRRNEKIA
          MAQDQGEKENPMRELRIRKLCLNI.VG.SGDRLT.AAKVLEQLTGQTPVFSKARY.VRSF..IRRNEKIA
Retrocopy MAQDQGEKENPMRELRIRKLCLNIFVGKSGDRLTQAAKVLEQLTGQTPVFSKARYIVRSFA<IRRNEKIA

Parental  VHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYDPSIGIYGLDFYVVLGRPGF
          VHCTV.GAKAEEILEKGLKVREYELRKNNFSDT.NFGFGIQEHIDLGIKYD.S.GIYGLDFYVVLGRPGF
Retrocopy VHCTVHGAKAEEILEKGLKVREYELRKNNFSDTSNFGFGIQEHIDLGIKYDLSVGIYGLDFYVVLGRPGF

Parental  SIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPGK
          SIADKKRRTG.IG.K.RISKEEAMRWFQQKYDGIILPGK
Retrocopy SIADKKRRTGFIGVKRRISKEEAMRWFQQKYDGIILPGK

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
SRP017611_brain	0.29 RPM	83.97 RPM
SRP017611_kidney	0.28 RPM	139.63 RPM
SRP017611_liver	0.20 RPM	96.28 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2690 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2690 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2690 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 29 parental genes, and 96 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005058	1 retrocopy	retro_acar_165,
Ailuropoda melanoleuca	ENSAMEG00000009704	3 retrocopies	retro_amel_1123, retro_amel_1754, retro_amel_234,
Bos taurus	ENSBTAG00000020905	1 retrocopy	retro_btau_267,
Canis familiaris	ENSCAFG00000013232	2 retrocopies	retro_cfam_1059, retro_cfam_543,
Callithrix jacchus	ENSCJAG00000020953	1 retrocopy	retro_cjac_790,
Cavia porcellus	ENSCPOG00000008432	2 retrocopies	retro_cpor_261, retro_cpor_788,
Dasypus novemcinctus	ENSDNOG00000011230	2 retrocopies	retro_dnov_1453, retro_dnov_605,
Dipodomys ordii	ENSDORG00000012496	1 retrocopy	retro_dord_143,
Equus caballus	ENSECAG00000021136	3 retrocopies	retro_ecab_471, retro_ecab_669, retro_ecab_926,
Echinops telfairi	ENSETEG00000014825	8 retrocopies	retro_etel_1054, retro_etel_136, retro_etel_1452, retro_etel_1893, retro_etel_2018, retro_etel_500, retro_etel_62, retro_etel_948,
Felis catus	ENSFCAG00000028651	2 retrocopies	retro_fcat_1069, retro_fcat_1877,
Homo sapiens	ENSG00000142676	6 retrocopies	retro_hsap_1159, retro_hsap_1801, retro_hsap_2272, retro_hsap_3238, retro_hsap_606, retro_hsap_712,
Gorilla gorilla	ENSGGOG00000014628	6 retrocopies	retro_ggor_1192, retro_ggor_1325, retro_ggor_1690, retro_ggor_2204, retro_ggor_533, retro_ggor_603,
Loxodonta africana	ENSLAFG00000030853	2 retrocopies	retro_lafr_371, retro_lafr_434,
Macropus eugenii	ENSMEUG00000013738	3 retrocopies	retro_meug_488, retro_meug_517, retro_meug_633,
Myotis lucifugus	ENSMLUG00000008868	3 retrocopies	retro_mluc_1271, retro_mluc_1345, retro_mluc_2321,
Macaca mulatta	ENSMMUG00000002445	3 retrocopies	retro_mmul_2039, retro_mmul_2415, retro_mmul_2462,
Monodelphis domestica	ENSMODG00000012828	1 retrocopy	retro_mdom_641,
Mus musculus	ENSMUSG00000059291	3 retrocopies	retro_mmus_144, retro_mmus_146, retro_mmus_78,
Ornithorhynchus anatinus	ENSOANG00000000321	1 retrocopy	retro_oana_49,
Otolemur garnettii	ENSOGAG00000032741	6 retrocopies	retro_ogar_1325, retro_ogar_1935, retro_ogar_1963, retro_ogar_2322, retro_ogar_2630, retro_ogar_569,
Pongo abelii	ENSPPYG00000001736	6 retrocopies	retro_pabe_1478, retro_pabe_1946, retro_pabe_2686, retro_pabe_612, retro_pabe_615, retro_pabe_964,
Pteropus vampyrus	ENSPVAG00000004282	1 retrocopy	retro_pvam_1068,
Rattus norvegicus	ENSRNOG00000026260	9 retrocopies	retro_rnor_1735, retro_rnor_2287, retro_rnor_2314, retro_rnor_2690 , retro_rnor_271, retro_rnor_2725, retro_rnor_668, retro_rnor_795, retro_rnor_919,
Sarcophilus harrisii	ENSSHAG00000006767	1 retrocopy	retro_shar_638,
Sus scrofa	ENSSSCG00000024260	4 retrocopies	retro_sscr_1048, retro_sscr_1049, retro_sscr_1074, retro_sscr_819,
Tupaia belangeri	ENSTBEG00000007838	5 retrocopies	retro_tbel_2850, retro_tbel_3023, retro_tbel_3273, retro_tbel_4736, retro_tbel_596,
Tarsius syrichta	ENSTSYG00000001349	6 retrocopies	retro_tsyr_1138, retro_tsyr_127, retro_tsyr_1583, retro_tsyr_1605, retro_tsyr_516, retro_tsyr_520,
Tursiops truncatus	ENSTTRG00000016115	4 retrocopies	retro_ttru_1525, retro_ttru_1779, retro_ttru_476, retro_ttru_911,