RetrogeneDB ID: retro_sscr_887

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:125624177..125624612(-)
• Located in intron of: ENSSSCG00000003768

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS11
• Ensembl ID: ENSSSCG00000003165
• Aliases: None
• Description: Sus scrofa ribosomal protein S11 (RPS11), mRNA. [Source:RefSeq mRNA;Acc:NM_001244070]

Sequence

>retro_sscr_887
ACCGTCTTTCAAAATAAAAAGAGAGTCCTGCTTGGAGAAACTGTCATAGAGAAGTCTCCACAATACACGAACCCTGATCT
GGGCTTCAAGGCACCAGGGAGGACCATTGAGGACGCCTACACTGACAAGAAATGCCCCTTACTGGTAATGTCTGCAGCTG
AGGGCAGATCCTGTCTGGTATGGTGACCAAGATGAAGATGCAGAAGACCTTTGTTATCTTCCGAGACCACCTCCACTACA
TCTAGAAGTACAAAGCTTCCAGAACTGCTGTAAGAACACGCCCATGCACCTCTCCCCTGTGCTGCTGCTTCAGGGGCATC
CAGAGTGGTGACATCATCATGGTGGGTGAGTGCCGGCTCCTGAGCAACGCTGTGCAAGTTCAACATGCTCAAGATCCCCA
AGGTTGCCAGTACAAAGAAGTGATTCCAGAAATTC

Alignment

ORF - retro_sscr_887 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.14 %
• Parental protein coverage: 91.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKCPF-TGNVSIRGRILSGVVTKMKMQ
          T.FQNKKRVLLGET..EK.P.Y..N..LGFK.P...IE..Y.DKKCP..TGNV...G.ILSG.VTKMKMQ
Retrocopy TVFQNKKRVLLGETVIEKSPQY-TNPDLGFKAPGRTIEDAYTDKKCPL<TGNVCS*GQILSGMVTKMKMQ

Parental  RTIVIRRDYLHYIRKY--NRFEKRHKNMSVHLSPCFRDVQIGDIVTVGECRPLSKTV-RFNVLKVTKAAG
          .T.VI.RD.LHYI.KY...R...R.......L..CFR..Q.GDI..VGECR.LS..V..FN.LK..K.A.
Retrocopy KTFVIFRDHLHYI*KYKASRTAVRTRPCTSPLCCCFRGIQSGDIIMVGECRLLSNAV>KFNMLKIPKVAS

Parental  TKKQFQKF
          TKK.FQKF
Retrocopy TKK*FQKF

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	0.13 RPM	1613.61 RPM
SRP014902_testis	0.14 RPM	1679.39 RPM
SRP018288_heart	0.00 RPM	543.65 RPM
SRP018288_kidney	0.00 RPM	545.33 RPM
SRP018288_liver	0.00 RPM	444.39 RPM
SRP018288_lung	0.00 RPM	795.06 RPM
SRP018856_adipose	0.05 RPM	1972.04 RPM
SRP035408_brain	0.00 RPM	354.80 RPM
SRP035408_liver	0.06 RPM	315.66 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_887 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_887 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_887 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_1282
Equus caballus	retro_ecab_868

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 120 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014020	13 retrocopies	retro_amel_1038, retro_amel_1071, retro_amel_1398, retro_amel_1406, retro_amel_1475, retro_amel_246, retro_amel_262, retro_amel_317, retro_amel_64, retro_amel_757, retro_amel_759, retro_amel_764, retro_amel_859,
Bos taurus	ENSBTAG00000013924	5 retrocopies	retro_btau_1282, retro_btau_1369, retro_btau_1499, retro_btau_1529, retro_btau_888,
Canis familiaris	ENSCAFG00000003631	9 retrocopies	retro_cfam_126, retro_cfam_1333, retro_cfam_1572, retro_cfam_1656, retro_cfam_1669, retro_cfam_1900, retro_cfam_1955, retro_cfam_2121, retro_cfam_248,
Callithrix jacchus	ENSCJAG00000000069	1 retrocopy	retro_cjac_340,
Danio rerio	ENSDARG00000053058	1 retrocopy	retro_drer_15,
Dasypus novemcinctus	ENSDNOG00000016107	9 retrocopies	retro_dnov_1055, retro_dnov_1102, retro_dnov_1629, retro_dnov_1729, retro_dnov_188, retro_dnov_2520, retro_dnov_586, retro_dnov_68, retro_dnov_754,
Equus caballus	ENSECAG00000000370	1 retrocopy	retro_ecab_868,
Felis catus	ENSFCAG00000009196	13 retrocopies	retro_fcat_1362, retro_fcat_1491, retro_fcat_1535, retro_fcat_1564, retro_fcat_1719, retro_fcat_1945, retro_fcat_197, retro_fcat_1991, retro_fcat_273, retro_fcat_507, retro_fcat_792, retro_fcat_854, retro_fcat_995,
Gorilla gorilla	ENSGGOG00000002936	6 retrocopies	retro_ggor_1525, retro_ggor_2843, retro_ggor_2900, retro_ggor_292, retro_ggor_805, retro_ggor_842,
Myotis lucifugus	ENSMLUG00000030475	1 retrocopy	retro_mluc_539,
Macaca mulatta	ENSMMUG00000007549	6 retrocopies	retro_mmul_1147, retro_mmul_1856, retro_mmul_2464, retro_mmul_413, retro_mmul_634, retro_mmul_813,
Monodelphis domestica	ENSMODG00000013434	7 retrocopies	retro_mdom_1185, retro_mdom_1284, retro_mdom_1421, retro_mdom_1950, retro_mdom_636, retro_mdom_922, retro_mdom_978,
Otolemur garnettii	ENSOGAG00000004627	7 retrocopies	retro_ogar_1290, retro_ogar_1813, retro_ogar_1910, retro_ogar_2037, retro_ogar_2573, retro_ogar_2640, retro_ogar_840,
Pan troglodytes	ENSPTRG00000011299	1 retrocopy	retro_ptro_88,
Rattus norvegicus	ENSRNOG00000020595	18 retrocopies	retro_rnor_1132, retro_rnor_1159, retro_rnor_1261, retro_rnor_1299, retro_rnor_1363, retro_rnor_1414, retro_rnor_1435, retro_rnor_1451, retro_rnor_1635, retro_rnor_1790, retro_rnor_2000, retro_rnor_2647, retro_rnor_385, retro_rnor_394, retro_rnor_538, retro_rnor_737, retro_rnor_835, retro_rnor_989,
Sorex araneus	ENSSARG00000003236	2 retrocopies	retro_sara_11, retro_sara_469,
Sus scrofa	ENSSSCG00000003165	2 retrocopies	retro_sscr_432, retro_sscr_887 ,
Ictidomys tridecemlineatus	ENSSTOG00000023443	2 retrocopies	retro_itri_1033, retro_itri_805,
Tupaia belangeri	ENSTBEG00000016677	16 retrocopies	retro_tbel_125, retro_tbel_1361, retro_tbel_1753, retro_tbel_2071, retro_tbel_2207, retro_tbel_2808, retro_tbel_2947, retro_tbel_319, retro_tbel_3401, retro_tbel_3571, retro_tbel_3600, retro_tbel_3742, retro_tbel_449, retro_tbel_604, retro_tbel_801, retro_tbel_836,