RetrogeneDB ID: retro_sscr_1049

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 9:2142073..2142596(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL11
• Ensembl ID: ENSSSCG00000024260
• Aliases: None
• Description: ribosomal protein L11 [Source:HGNC Symbol;Acc:10301]

Sequence

>retro_sscr_1049
ATGGCGCAGGATCAAGGTGAAAAGGAGAACCCCACGAGGGAACCTCACATCCACAGGCTCTGCCTCAACATCTCTGAGGG
GGAGAGTGGAGACAGACTCACCTGGGCAGCCAGGTGCTGGAGCAGCTCACAGGCCAGACCCCTGCGTTCTGCAAAGCCAA
ATACACCATCAGATCCCTTGGCACCAGGAGAAAGGAAAAGGTTGCCGTCCGCTGCACAGTCCGTGGGACCGAGGGAGAAG
AAATACTTGAGAAAGGTCTGCAGGTGCAAGAGCGCGAGTTAAGAAAAATAACTTCCCAGACACTGGAAACTTTGGTTTGG
GGATCCAAGAACACATCAATCTGGGAATCAAATGTCACCCAAGTACCAGTATCTACAGCCTAGACTTCTACATGGTGCTG
GGTAGGCCAGGTTTCAGCATCGCAGACAAAAATCCCAGGACAGGCTGCACTGGGCCCCACAGAGTCAGCAAAGAGGAGGC
CATGTGCTGGTTCCAGCACAAGTACATCATCCTTCCCAGCAAG

Alignment

ORF - retro_sscr_1049 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAQDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAK-VLEQLTGQTPVFSKARYTVRSFGIRRNEKIA
          MAQDQGEKENP.RE..I..LCLNI..GESGDRLT.AA..VLEQLTGQTP.F.KA.YT.RS.G.RR.EK.A
Retrocopy MAQDQGEKENPTREPHIHRLCLNISEGESGDRLTWAAR<VLEQLTGQTPAFCKAKYTIRSLGTRRKEKVA

Parental  VHCTVRGAKAEEILEKGLKVREYELRK-NNFSDTGNFGFGIQEHIDLGIKYDPSIGIYGLDFYVVLGRPG
          V.CTVRG...EEILEKGL.V.E.ELRK.NNF.DTGNFG.GIQEHI.LGIK..PS..IY.LDFY.VLGRPG
Retrocopy VRCTVRGTEGEEILEKGLQVQERELRK<NNFPDTGNFGLGIQEHINLGIKCHPSTSIYSLDFYMVLGRPG

Parental  FSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPGK
          FSIADK..RTGC.G..HR.SKEEAM.WFQ.KY..IILP.K
Retrocopy FSIADKNPRTGCTG-PHRVSKEEAMCWFQHKY--IILPSK

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	424.61 RPM
SRP014902_testis	0.00 RPM	817.98 RPM
SRP018288_heart	0.00 RPM	505.59 RPM
SRP018288_kidney	0.00 RPM	371.46 RPM
SRP018288_liver	0.00 RPM	340.93 RPM
SRP018288_lung	0.00 RPM	913.07 RPM
SRP018856_adipose	0.00 RPM	1221.73 RPM
SRP035408_brain	0.00 RPM	357.62 RPM
SRP035408_liver	0.00 RPM	369.35 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1049 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1049 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1049 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 58 retrocopies.

Species	Parental gene accession	Retrocopies number
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,
Dasypus novemcinctus	ENSDNOG00000011230	2 retrocopies	retro_dnov_1453, retro_dnov_605,
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,
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,
Oryctolagus cuniculus	ENSOCUG00000022928	1 retrocopy	retro_ocun_1387,
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,
Sus scrofa	ENSSSCG00000024260	4 retrocopies	retro_sscr_1048, retro_sscr_1049 , retro_sscr_1074, retro_sscr_819,
Tarsius syrichta	ENSTSYG00000001349	6 retrocopies	retro_tsyr_1138, retro_tsyr_127, retro_tsyr_1583, retro_tsyr_1605, retro_tsyr_516, retro_tsyr_520,