RetrogeneDB ID: retro_sscr_172

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:123561481..123561737(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPE
• Ensembl ID: ENSSSCG00000023562
• Aliases: SNRPE, Sm-E, SmE, snRNP-E
• Description: small nuclear ribonucleoprotein polypeptide E [Source:HGNC Symbol;Acc:11161]

Sequence

>retro_sscr_172
ATGGTGTACCATGGCCAGGGCCAGAGAGTGCAGAAAGCAATGGTGCAGCCCATCAACTTCATCTTCAGATACTTGCAAAA
TAGATCTCGGATTCAGGTGTGGCTTTTGAGAAAGTGAATATGTGCATTGAGGGCTGTATCACTGGTTTTGATGAGTATGT
GAACTTTGCATTAGATATGTAGAAGAGATTCATTCTAAGATAAAGTCAAGAAAATGACTGGGTCAAAAGAAAAAAACTGG
GTCAGATTATGCTATA

Alignment

ORF - retro_sscr_172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.18 %
• Parental protein coverage: 93.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAYRGQGQKVQKVMVQPINLIFRYLQNRSRIQVWL-YEQVNMRIEGCIIGFDEYMNLVLD-DAEEIHSKT
          M.Y.GQGQ.VQK.MVQPIN.IFRYLQNRSRIQVWL..E.VNM.IEGCI.GFDEY.N..LD...EEIHSK.
Retrocopy MVYHGQGQRVQKAMVQPINFIFRYLQNRSRIQVWL<FEKVNMCIEGCITGFDEYVNFALD<YVEEIHSKI

Parental  KSRKQLGRIMLKGDNITL
          KSRK.LG.....G.....
Retrocopy KSRK*LGQKKKTGSDYAI

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	11.41 RPM
SRP014902_testis	0.00 RPM	46.96 RPM
SRP018288_heart	0.00 RPM	33.13 RPM
SRP018288_kidney	0.00 RPM	33.39 RPM
SRP018288_liver	0.00 RPM	32.14 RPM
SRP018288_lung	0.00 RPM	11.71 RPM
SRP018856_adipose	0.00 RPM	18.56 RPM
SRP035408_brain	0.00 RPM	30.33 RPM
SRP035408_liver	0.00 RPM	36.61 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_172 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_172 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_172 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 91 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006735	1 retrocopy	retro_cjac_3163,
Dasypus novemcinctus	ENSDNOG00000004490	24 retrocopies	retro_dnov_1009, retro_dnov_1141, retro_dnov_122, retro_dnov_1223, retro_dnov_1312, retro_dnov_1314, retro_dnov_1362, retro_dnov_1438, retro_dnov_163, retro_dnov_191, retro_dnov_2398, retro_dnov_2671, retro_dnov_360, retro_dnov_414, retro_dnov_513, retro_dnov_579, retro_dnov_796, retro_dnov_828, retro_dnov_898, retro_dnov_900, retro_dnov_902, retro_dnov_93, retro_dnov_967, retro_dnov_983,
Echinops telfairi	ENSETEG00000014015	24 retrocopies	retro_etel_1136, retro_etel_1244, retro_etel_138, retro_etel_1443, retro_etel_1530, retro_etel_1636, retro_etel_1739, retro_etel_1781, retro_etel_1947, retro_etel_2143, retro_etel_234, retro_etel_258, retro_etel_310, retro_etel_377, retro_etel_466, retro_etel_546, retro_etel_56, retro_etel_579, retro_etel_581, retro_etel_582, retro_etel_76, retro_etel_776, retro_etel_799, retro_etel_80,
Gorilla gorilla	ENSGGOG00000000755	7 retrocopies	retro_ggor_1462, retro_ggor_1626, retro_ggor_1700, retro_ggor_2221, retro_ggor_228, retro_ggor_2892, retro_ggor_91,
Myotis lucifugus	ENSMLUG00000013244	8 retrocopies	retro_mluc_1639, retro_mluc_1650, retro_mluc_1994, retro_mluc_2045, retro_mluc_2088, retro_mluc_2326, retro_mluc_85, retro_mluc_919,
Mustela putorius furo	ENSMPUG00000011642	7 retrocopies	retro_mputfur_1078, retro_mputfur_1527, retro_mputfur_1634, retro_mputfur_53, retro_mputfur_638, retro_mputfur_729, retro_mputfur_949,
Pongo abelii	ENSPPYG00000000326	8 retrocopies	retro_pabe_1375, retro_pabe_20, retro_pabe_2023, retro_pabe_228, retro_pabe_3015, retro_pabe_3620, retro_pabe_56, retro_pabe_610,
Sorex araneus	ENSSARG00000003311	9 retrocopies	retro_sara_171, retro_sara_173, retro_sara_183, retro_sara_214, retro_sara_219, retro_sara_37, retro_sara_664, retro_sara_697, retro_sara_750,
Sus scrofa	ENSSSCG00000023562	3 retrocopies	retro_sscr_1159, retro_sscr_172 , retro_sscr_606,