RetrogeneDB ID: retro_sscr_849

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:104988922..104989235(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL36
• Ensembl ID: ENSSSCG00000030010
• Aliases: None
• Description: ribosomal protein L36 [Source:HGNC Symbol;Acc:13631]

Sequence

>retro_sscr_849
ATGGCTCTGCACTCTCCCATGCCTGTGGGCCTCAGCAAGGGCCACAGGTGACCAAGAACGTGAGCAAACTGAGGCAGAGC
TGCCTCGGGCACCTCACTGAGCACAGCAAGTTGGTGGAGGACAGGTTCCGGGAGCTATGCAGCTTTTTGCCTTATGAGGT
GTGGGCCATAATGCTTCTCCAGGTCTCCAAGGACAAGTTGAGCCCTCAAGTTCATCAAGAAAAGGGTGGGGACATACATC
TATGGCAAGAGGAAGAGAAAGGTACTGAGTAGTGTCCTTGGCAGCCATAAGGAAAGGGGCAGCCAAGAAGGAC

Alignment

ORF - retro_sscr_849 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.74 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MALRYPMAVGLNKGHK-VTKNVSKPRHSRRRGRLTKHTKFVRDMIREVCGFAPYERRAMELLKVSKDKR-
          MAL..PM.VGL.KGH..VTKNVSK.R.S...G.LT.H.K.V.D..RE.C.F.PYE..A..LL.VSKDK..
Retrocopy MALHSPMPVGLSKGHR<VTKNVSKLRQSCL-GHLTEHSKLVEDRFRELCSFLPYEVWAIMLLQVSKDKL>

Parental  ALKFIKKRVGTHIRAKRKREELSNV-LAAMRKAAAKKD
          ALKFIKKRVGT.I..KRKR..LS.V.LAA.RK.AAKKD
Retrocopy ALKFIKKRVGTYIYGKRKRKVLSSV>LAAIRKGAAKKD

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
SRP014902_placenta	0.00 RPM	193.12 RPM
SRP014902_testis	0.00 RPM	515.29 RPM
SRP018288_heart	0.00 RPM	164.23 RPM
SRP018288_kidney	0.00 RPM	193.27 RPM
SRP018288_liver	0.00 RPM	179.42 RPM
SRP018288_lung	0.00 RPM	352.62 RPM
SRP018856_adipose	0.00 RPM	288.10 RPM
SRP035408_brain	0.00 RPM	198.53 RPM
SRP035408_liver	0.00 RPM	186.64 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_849 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_849 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_849 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 114 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012349	6 retrocopies	retro_amel_1222, retro_amel_1581, retro_amel_1935, retro_amel_748, retro_amel_799, retro_amel_835,
Bos taurus	ENSBTAG00000001794	3 retrocopies	retro_btau_139, retro_btau_238, retro_btau_81,
Callithrix jacchus	ENSCJAG00000017072	2 retrocopies	retro_cjac_280, retro_cjac_52,
Cavia porcellus	ENSCPOG00000022839	3 retrocopies	retro_cpor_1317, retro_cpor_1343, retro_cpor_857,
Dasypus novemcinctus	ENSDNOG00000005163	8 retrocopies	retro_dnov_19, retro_dnov_2160, retro_dnov_311, retro_dnov_313, retro_dnov_457, retro_dnov_578, retro_dnov_595, retro_dnov_631,
Felis catus	ENSFCAG00000011838	5 retrocopies	retro_fcat_1152, retro_fcat_1168, retro_fcat_1216, retro_fcat_406, retro_fcat_94,
Homo sapiens	ENSG00000130255	13 retrocopies	retro_hsap_1059, retro_hsap_1440, retro_hsap_2000, retro_hsap_2434, retro_hsap_2577, retro_hsap_3051, retro_hsap_3248, retro_hsap_3769, retro_hsap_3892, retro_hsap_396, retro_hsap_4211, retro_hsap_4742, retro_hsap_534,
Gorilla gorilla	ENSGGOG00000015365	11 retrocopies	retro_ggor_1514, retro_ggor_1613, retro_ggor_180, retro_ggor_2211, retro_ggor_2535, retro_ggor_2620, retro_ggor_34, retro_ggor_487, retro_ggor_60, retro_ggor_82, retro_ggor_885,
Latimeria chalumnae	ENSLACG00000015161	1 retrocopy	retro_lcha_47,
Macropus eugenii	ENSMEUG00000002743	4 retrocopies	retro_meug_1318, retro_meug_176, retro_meug_261, retro_meug_283,
Monodelphis domestica	ENSMODG00000001275	2 retrocopies	retro_mdom_1353, retro_mdom_148,
Mustela putorius furo	ENSMPUG00000006166	6 retrocopies	retro_mputfur_1423, retro_mputfur_150, retro_mputfur_1562, retro_mputfur_747, retro_mputfur_749, retro_mputfur_773,
Mus musculus	ENSMUSG00000057863	9 retrocopies	retro_mmus_151, retro_mmus_1601, retro_mmus_1900, retro_mmus_1912, retro_mmus_193, retro_mmus_2864, retro_mmus_3379, retro_mmus_38, retro_mmus_652,
Otolemur garnettii	ENSOGAG00000027049	12 retrocopies	retro_ogar_1348, retro_ogar_18, retro_ogar_184, retro_ogar_2256, retro_ogar_2278, retro_ogar_2332, retro_ogar_2537, retro_ogar_2592, retro_ogar_3278, retro_ogar_358, retro_ogar_795, retro_ogar_888,
Pongo abelii	ENSPPYG00000009431	12 retrocopies	retro_pabe_1194, retro_pabe_137, retro_pabe_1639, retro_pabe_1792, retro_pabe_1834, retro_pabe_1898, retro_pabe_216, retro_pabe_3081, retro_pabe_3173, retro_pabe_318, retro_pabe_3443, retro_pabe_3688,
Rattus norvegicus	ENSRNOG00000033473	5 retrocopies	retro_rnor_11, retro_rnor_17, retro_rnor_170, retro_rnor_369, retro_rnor_687,
Sarcophilus harrisii	ENSSHAG00000013492	8 retrocopies	retro_shar_185, retro_shar_347, retro_shar_543, retro_shar_557, retro_shar_592, retro_shar_615, retro_shar_716, retro_shar_819,
Sus scrofa	ENSSSCG00000030010	2 retrocopies	retro_sscr_849 , retro_sscr_960,
Ictidomys tridecemlineatus	ENSSTOG00000020518	2 retrocopies	retro_itri_43, retro_itri_593,