RetrogeneDB ID: retro_sscr_350

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:168177266..168177773(+)
• Located in intron of: ENSSSCG00000011965

Retrocopy information

• Ensembl ID: ENSSSCG00000011966
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNRPN
• Ensembl ID: ENSSSCG00000028124
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptide N [Source:HGNC Symbol;Acc:11164]

Sequence

>retro_sscr_350
CAAAACAAGAGGAGAGAGAAGCAAGTCCTCGGTCTGGTGCTACTTCGAGGGGAGAACCTGGTCTCAATGACAGTAGAGGG
ACCACCTCCCAAAGATACCAGTGTTGCCCTAGTGCCGCTAGCTGGGGGCCCAGGGATTGGCAGAGCTGCTGTCAGGGGAA
TCCCAGCCAATGTTCCTATGCCCCAGGCTCCTGCAGGACTTGCTGGGCCAGTCTGTGGGGTTGGTGGGCCATCCCAACAG
GTGATTACCCTGCAAGGAAGAGGCACTGTTGCAGCAGCTGCAGCTGCTGCTACAGCCAGTATTGCAGGGGCCCCAACCCA
GTACCCACCTGGCCGAGCAGGTCCTCCCCAACCTATGGGCCGAGGAGCACCCCCTCCAGGCATGATGGGCCCAACTCCTG
GTATGAGGCCTCCTATGGGTCCCCCAGTGGGAATCACCCCTGGAAGAGGAACTCCAATGGGCATGCCCCCACCCGCCATG
CGGCCCCCTCCCCCAGGGATACGAGGC

Alignment

ORF - retro_sscr_350 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.65 %
• Parental protein coverage: 71.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QPEREEKRVLGLVLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGVGRAAGRGVPAGVPIPQAPAGL
          Q..R.EK.VLGLVLLRGENLVSMTVEGPPPKDT..A.VPL...AGGPG.GRAA.RG.PA.VP.PQAPAGL
Retrocopy QNKRREKQVLGLVLLRGENLVSMTVEGPPPKDTSVALVPL---AGGPGIGRAAVRGIPANVPMPQAPAGL

Parental  AGPVRGVGGPSQQVMTPQGRGTVAAAAVAATASIAGAPTQYPPGRGTPPTPVGRATPPPGIMAPPPGMSP
          AGPV.GVGGPSQQV.T.QGRGTVAAAA.AATASIAGAPTQYPPGR..PP.P.GR..PPPG.M.P.PGM.P
Retrocopy AGPVCGVGGPSQQVITLQGRGTVAAAAAAATASIAGAPTQYPPGRAGPPQPMGRGAPPPGMMGPTPGMRP

Parental  PMGPPIGLPPTRGTPIGMPPPGMRPPPPGIRG
          PMGPP.G..P.RGTP.GMPPP.MRPPPPGIRG
Retrocopy PMGPPVGITPGRGTPMGMPPPAMRPPPPGIRG

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	13.67 RPM	12.48 RPM
SRP014902_testis	14.14 RPM	44.98 RPM
SRP018288_heart	0.65 RPM	50.13 RPM
SRP018288_kidney	6.01 RPM	72.70 RPM
SRP018288_liver	4.80 RPM	4.64 RPM
SRP018288_lung	8.96 RPM	17.21 RPM
SRP018856_adipose	1.44 RPM	27.18 RPM
SRP035408_brain	3.87 RPM	436.17 RPM
SRP035408_liver	4.08 RPM	18.08 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_350 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_350 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_350 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007034	3 retrocopies	retro_amel_1048, retro_amel_714, retro_amel_839,
Bos taurus	ENSBTAG00000008251	1 retrocopy	retro_btau_620,
Canis familiaris	ENSCAFG00000010127	6 retrocopies	retro_cfam_1753, retro_cfam_1874, retro_cfam_2039, retro_cfam_627, retro_cfam_682, retro_cfam_752,
Choloepus hoffmanni	ENSCHOG00000001846	2 retrocopies	retro_chof_2275, retro_chof_385,
Cavia porcellus	ENSCPOG00000020270	1 retrocopy	retro_cpor_878,
Felis catus	ENSFCAG00000022298	2 retrocopies	retro_fcat_1390, retro_fcat_1895,
Homo sapiens	ENSG00000128739	1 retrocopy	retro_hsap_2580,
Gorilla gorilla	ENSGGOG00000003988	1 retrocopy	retro_ggor_1615,
Loxodonta africana	ENSLAFG00000009458	1 retrocopy	retro_lafr_1012,
Myotis lucifugus	ENSMLUG00000023361	3 retrocopies	retro_mluc_1192, retro_mluc_1816, retro_mluc_2156,
Macaca mulatta	ENSMMUG00000023139	1 retrocopy	retro_mmul_644,
Mustela putorius furo	ENSMPUG00000014638	1 retrocopy	retro_mputfur_1080,
Mus musculus	ENSMUSG00000000948	3 retrocopies	retro_mmus_1285, retro_mmus_1733, retro_mmus_665,
Oryctolagus cuniculus	ENSOCUG00000003532	4 retrocopies	retro_ocun_1291, retro_ocun_488, retro_ocun_689, retro_ocun_846,
Otolemur garnettii	ENSOGAG00000007392	5 retrocopies	retro_ogar_1179, retro_ogar_3042, retro_ogar_3060, retro_ogar_475, retro_ogar_722,
Pongo abelii	ENSPPYG00000006269	1 retrocopy	retro_pabe_1900,
Pan troglodytes	ENSPTRG00000006826	1 retrocopy	retro_ptro_1507,
Rattus norvegicus	ENSRNOG00000015976	6 retrocopies	retro_rnor_1122, retro_rnor_1314, retro_rnor_1485, retro_rnor_2161, retro_rnor_2462, retro_rnor_2517,
Sus scrofa	ENSSSCG00000028124	2 retrocopies	retro_sscr_350 , retro_sscr_405,
Ictidomys tridecemlineatus	ENSSTOG00000001339	1 retrocopy	retro_itri_44,
Tursiops truncatus	ENSTTRG00000010966	5 retrocopies	retro_ttru_1005, retro_ttru_1051, retro_ttru_1473, retro_ttru_580, retro_ttru_600,