RetrogeneDB ID: retro_sscr_151

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:18518998..18519153(-)
• Located in intron of: ENSSSCG00000004101

Retrocopy information

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

Parental gene information

• Parental gene symbol: C14orf2
• Ensembl ID: ENSSSCG00000002550
• Aliases: None
• Description: chromosome 14 open reading frame 2 [Source:HGNC Symbol;Acc:1188]

Sequence

>retro_sscr_151
GTTTGGATCCCCATGAGGCCCTGCTATACCCGAGTTCACCATGAAATTTGGGTAGGAATGGGGTTGATGGCTTCACCGTT
TATAAAATCAGGAGTGCTGATAAAAGAAGTAAAACCTTGAAAGCTCCCAGTCCTGTGCCTGCTCATGGGCATCAT

Alignment

ORF - retro_sscr_151 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.25 %
• Parental protein coverage: 86.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VWIPLKPYYTQVYQEIWVGMGLM-GFIVYKIRSADKRSKALKASSPAPAHGHH
          VWIP..P.YT.V..EIWVGMGLM.GF.VYKIRSADKRSK.LKA.SP.PAHGHH
Retrocopy VWIPMRPCYTRVHHEIWVGMGLM<GFTVYKIRSADKRSKTLKAPSPVPAHGHH

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	111.49 RPM
SRP014902_testis	0.00 RPM	42.43 RPM
SRP018288_heart	0.00 RPM	121.35 RPM
SRP018288_kidney	0.00 RPM	131.50 RPM
SRP018288_liver	0.00 RPM	65.08 RPM
SRP018288_lung	0.00 RPM	14.05 RPM
SRP018856_adipose	0.00 RPM	73.77 RPM
SRP035408_brain	0.03 RPM	61.36 RPM
SRP035408_liver	0.00 RPM	70.63 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_151 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_151 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_151 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000026886	4 retrocopies	retro_btau_1496, retro_btau_1629, retro_btau_818, retro_btau_925,
Homo sapiens	ENSG00000156411	1 retrocopy	retro_hsap_3993,
Mustela putorius furo	ENSMPUG00000002297	9 retrocopies	retro_mputfur_1068, retro_mputfur_1180, retro_mputfur_1395, retro_mputfur_1456, retro_mputfur_1500, retro_mputfur_1635, retro_mputfur_243, retro_mputfur_432, retro_mputfur_981,
Nomascus leucogenys	ENSNLEG00000016248	1 retrocopy	retro_nleu_542,
Pan troglodytes	ENSPTRG00000006764	1 retrocopy	retro_ptro_2710,
Pteropus vampyrus	ENSPVAG00000011548	3 retrocopies	retro_pvam_39, retro_pvam_504, retro_pvam_938,
Rattus norvegicus	ENSRNOG00000043144	2 retrocopies	retro_rnor_116, retro_rnor_14,
Sus scrofa	ENSSSCG00000002550	5 retrocopies	retro_sscr_151 , retro_sscr_483, retro_sscr_484, retro_sscr_517, retro_sscr_732,
Tupaia belangeri	ENSTBEG00000008996	3 retrocopies	retro_tbel_1138, retro_tbel_3782, retro_tbel_3854,
Tursiops truncatus	ENSTTRG00000006404	5 retrocopies	retro_ttru_1417, retro_ttru_1457, retro_ttru_1722, retro_ttru_1924, retro_ttru_271,
Vicugna pacos	ENSVPAG00000001249	7 retrocopies	retro_vpac_152, retro_vpac_347, retro_vpac_517, retro_vpac_526, retro_vpac_545, retro_vpac_577, retro_vpac_610,