RetrogeneDB ID: retro_sscr_1124

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: GL896216.1:10703..11044(+)
• Located in intron of: ENSSSCG00000020993

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCNP
• Ensembl ID: ENSSSCG00000011955
• Aliases: None
• Description: PEST proteolytic signal containing nuclear protein [Source:HGNC Symbol;Acc:30023]

Sequence

>retro_sscr_1124
GAGAAGCCTGAGAAGCTGCAGCAAGTGGAGTAATGGAGTAATGAAGGGGGAAGCTCCAGTTGCAGAGCGGAGAAGCAGTC
AGCTGAAGAAGAAGCTGCAGACCTCCCAAGAAAACCTGAAAAGATCTCTAACTTTGGTTTTGCCATAGGTAGTCACACGA
CAAAGAAAGCCTCTGCCATATCCATCAAACTGGCTGAAGGAAGCCTAAAGAAACTGTTCCGACTCTTGCTCCAAAAGCCC
TTTCAGTAGCAGCAGCTTTTAATGAAGATGAAGATAGTGAGCAAGAGGAAATGCCTCCAGAAGCCAAGGTGAGGATAAAG
AATATTGGAAGGGATACACCA

Alignment

ORF - retro_sscr_1124 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 63.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKPVKTKTVS-SSNGGESSSRSAEKRSAEEEAADLPTKPTKISKFGFAIGSQTTKKASAISIKL-GSTKP
          EKP.K...V...SN.G.SSS..AEK.SAEEEAADLP.KP.KIS.FGFAIGS.TTKKASAISIKL.G..KP
Retrocopy EKPEKLQQVE*WSNEGGSSSCRAEKQSAEEEAADLPRKPEKISNFGFAIGSHTTKKASAISIKL<G*RKP

Parental  KETVPTLAPKTLSVAAAFNEDEDSEPEEMPPEAKMRMKNIGRDTP
          KETVPTLAPK.LSVAAAFNEDEDSE.EEMPPEAK.R.KNIGRDTP
Retrocopy KETVPTLAPKALSVAAAFNEDEDSEQEEMPPEAKVRIKNIGRDTP

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	6.64 RPM
SRP014902_testis	0.00 RPM	17.54 RPM
SRP018288_heart	0.00 RPM	30.57 RPM
SRP018288_kidney	0.10 RPM	28.07 RPM
SRP018288_liver	0.00 RPM	18.39 RPM
SRP018288_lung	0.71 RPM	37.57 RPM
SRP018856_adipose	0.05 RPM	30.57 RPM
SRP035408_brain	0.00 RPM	16.86 RPM
SRP035408_liver	0.00 RPM	21.90 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1124 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1124 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1124 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003777	2 retrocopies	retro_amel_1086, retro_amel_1679,
Canis familiaris	ENSCAFG00000009593	3 retrocopies	retro_cfam_1850, retro_cfam_2074, retro_cfam_2160,
Choloepus hoffmanni	ENSCHOG00000007972	11 retrocopies	retro_chof_1170, retro_chof_1215, retro_chof_2070, retro_chof_2280, retro_chof_2290, retro_chof_2553, retro_chof_2575, retro_chof_594, retro_chof_651, retro_chof_806, retro_chof_819,
Callithrix jacchus	ENSCJAG00000000508	6 retrocopies	retro_cjac_101, retro_cjac_1569, retro_cjac_1722, retro_cjac_3205, retro_cjac_3332, retro_cjac_401,
Dasypus novemcinctus	ENSDNOG00000008873	5 retrocopies	retro_dnov_1606, retro_dnov_259, retro_dnov_370, retro_dnov_910, retro_dnov_98,
Felis catus	ENSFCAG00000029026	2 retrocopies	retro_fcat_1767, retro_fcat_1822,
Gorilla gorilla	ENSGGOG00000025423	4 retrocopies	retro_ggor_882, retro_ggor_901, retro_ggor_902, retro_ggor_994,
Loxodonta africana	ENSLAFG00000005518	2 retrocopies	retro_lafr_1189, retro_lafr_458,
Myotis lucifugus	ENSMLUG00000005878	5 retrocopies	retro_mluc_1010, retro_mluc_1818, retro_mluc_2423, retro_mluc_603, retro_mluc_816,
Macaca mulatta	ENSMMUG00000017782	3 retrocopies	retro_mmul_1312, retro_mmul_1377, retro_mmul_2598,
Mustela putorius furo	ENSMPUG00000011696	1 retrocopy	retro_mputfur_850,
Oryctolagus cuniculus	ENSOCUG00000011110	7 retrocopies	retro_ocun_1072, retro_ocun_1144, retro_ocun_1496, retro_ocun_1537, retro_ocun_573, retro_ocun_687, retro_ocun_868,
Procavia capensis	ENSPCAG00000007007	3 retrocopies	retro_pcap_161, retro_pcap_194, retro_pcap_273,
Pteropus vampyrus	ENSPVAG00000009886	2 retrocopies	retro_pvam_1277, retro_pvam_421,
Sorex araneus	ENSSARG00000001433	2 retrocopies	retro_sara_265, retro_sara_626,
Sus scrofa	ENSSSCG00000011955	5 retrocopies	retro_sscr_1030, retro_sscr_1124 , retro_sscr_451, retro_sscr_696, retro_sscr_728,
Tursiops truncatus	ENSTTRG00000015008	1 retrocopy	retro_ttru_1167,
Vicugna pacos	ENSVPAG00000012239	1 retrocopy	retro_vpac_564,