RetrogeneDB ID: retro_sscr_117

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:94449278..94449745(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000029848
• Aliases: None
• Description: None

Sequence

>retro_sscr_117
ATGTCCATGGTGCCGCCCGGTCGCTCACAGACCAGCTGGCCCCGGGGGGTTTACCAATATGGCAACAAGTACATCCAGCA
GACCAAGCCCCTTAGCCTCGTGCTCACCATAAACCTGTACCCTCTTATTAATTATACTTTTGGTACAAAAGAGCCCCTGT
ATGAGAAGGACAGCTTTGTTGCCGCCAGATTTCAGTGCATGAGCGAGGAATTTGATAAATTTGGCATGAGGAGGACTGTA
GAAGTGGTTTTGATTGTCCATGAGCACCAGCTCCCCATGTGTTACTGCTACAGCTGGGAACAACTTTCCTCAAATTACCT
GATAGTGAGCTTAACCCAGGAGAAGATGAAATTGAAGGATTAAGACGCTTAATGACAGAGATACTGGGCTGTCAAGATGG
AGTCCTGCAAGACTGGGTCACTGACGATTGTTTTGGTAGATGGTGGAGACCAACTTTTGAACATCCT

Alignment

ORF - retro_sscr_117 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.08 %
• Parental protein coverage: 89.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSVVPPNRSQTGWPRGVNQYGNKYIQQTKPLSLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREE
          MS.VPP.RSQT.WPRGV.QYGNKYIQQTKPLSL..TINLYPL.NYTFGTKEPLYEKDS.VAARFQ.M.EE
Retrocopy MSMVPPGRSQTSWPRGVYQYGNKYIQQTKPLSLVLTINLYPLINYTFGTKEPLYEKDSFVAARFQCMSEE

Parental  FDKIGMRRTVEGVLIVHEHRL-PHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDW
          FDK.GMRRTVE.VLIVHEH.L.PHVLLLQLGTTF.KLP..ELNPGEDE.EGL.RLMTEILG.QDGVLQDW
Retrocopy FDKFGMRRTVEVVLIVHEHQL<PHVLLLQLGTTFLKLPDSELNPGEDEIEGLRRLMTEILGCQDGVLQDW

Parental  VIDDCIGNWWRPNFEPP
          V.DDC.G.WWRP.FE.P
Retrocopy VTDDCFGRWWRPTFEHP

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	15.40 RPM
SRP014902_testis	0.00 RPM	17.54 RPM
SRP018288_heart	0.00 RPM	12.49 RPM
SRP018288_kidney	0.00 RPM	21.28 RPM
SRP018288_liver	0.00 RPM	15.51 RPM
SRP018288_lung	0.00 RPM	26.78 RPM
SRP018856_adipose	0.00 RPM	18.46 RPM
SRP035408_brain	0.00 RPM	8.07 RPM
SRP035408_liver	0.00 RPM	9.01 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_117 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_117 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_117 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016628	1 retrocopy	retro_amel_540,
Bos taurus	ENSBTAG00000010207	2 retrocopies	retro_btau_1655, retro_btau_937,
Callithrix jacchus	ENSCJAG00000012724	3 retrocopies	retro_cjac_1121, retro_cjac_2211, retro_cjac_4100,
Cavia porcellus	ENSCPOG00000003705	1 retrocopy	retro_cpor_1054,
Equus caballus	ENSECAG00000001043	1 retrocopy	retro_ecab_292,
Erinaceus europaeus	ENSEEUG00000003402	1 retrocopy	retro_eeur_35,
Echinops telfairi	ENSETEG00000013634	1 retrocopy	retro_etel_622,
Felis catus	ENSFCAG00000008669	1 retrocopy	retro_fcat_1843,
Loxodonta africana	ENSLAFG00000028465	1 retrocopy	retro_lafr_610,
Myotis lucifugus	ENSMLUG00000004968	2 retrocopies	retro_mluc_1576, retro_mluc_999,
Macaca mulatta	ENSMMUG00000019906	1 retrocopy	retro_mmul_1360,
Mustela putorius furo	ENSMPUG00000003451	1 retrocopy	retro_mputfur_158,
Mus musculus	ENSMUSG00000031754	3 retrocopies	retro_mmus_1949, retro_mmus_1950, retro_mmus_2142,
Nomascus leucogenys	ENSNLEG00000001963	2 retrocopies	retro_nleu_1477, retro_nleu_2493,
Oryctolagus cuniculus	ENSOCUG00000017224	2 retrocopies	retro_ocun_154, retro_ocun_87,
Otolemur garnettii	ENSOGAG00000014888	2 retrocopies	retro_ogar_1450, retro_ogar_630,
Ochotona princeps	ENSOPRG00000006689	1 retrocopy	retro_opri_637,
Pteropus vampyrus	ENSPVAG00000014583	2 retrocopies	retro_pvam_533, retro_pvam_711,
Sorex araneus	ENSSARG00000006493	2 retrocopies	retro_sara_161, retro_sara_580,
Sarcophilus harrisii	ENSSHAG00000009651	1 retrocopy	retro_shar_469,
Sus scrofa	ENSSSCG00000029848	2 retrocopies	retro_sscr_117 , retro_sscr_185,
Tupaia belangeri	ENSTBEG00000007664	1 retrocopy	retro_tbel_4003,
Tarsius syrichta	ENSTSYG00000014602	4 retrocopies	retro_tsyr_1685, retro_tsyr_1888, retro_tsyr_790, retro_tsyr_988,
Tursiops truncatus	ENSTTRG00000013545	1 retrocopy	retro_ttru_1087,
Vicugna pacos	ENSVPAG00000003701	2 retrocopies	retro_vpac_340, retro_vpac_605,