RetrogeneDB ID: retro_sscr_171

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:122631013..122631499(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UFC1
• Ensembl ID: ENSSSCG00000006363
• Aliases: None
• Description: ubiquitin-fold modifier conjugating enzyme 1 [Source:HGNC Symbol;Acc:26941]

Sequence

>retro_sscr_171
ATGGCAGATGAGGCCACCTGGCATGTCACGTCTGAGATCCTGGTGCTGAAGATCAACACTGGTTCTCGAGATTGGGAGCT
GTGGGTACAGAGACTCAAGGAGGAACACCAGCCTCTTATTTGGTATGAGAAGAATAAGAATGCAGACAATGATTGGTTCT
GACCAGAGCCCAACAAGAAAGGGACTCGGTGGTCTGGAAAATGCTGGTACATCCACGACCTCCTCAAATATGAGCTTGAC
ATTCCTATCACATATCCTACTACTGCTCCAGAATCTGCAGTCCCTGAACTGGATGGAAAAACAGCAAAGATGTACAGCGA
TAGAAAAATATGCCTGAAAGATCACTTTCAGCCTTTATGTGCCAGAAACATGCCTGGGTTTGGACTAGCTCATCTCCTGG
CTATGGGACTGGGTCCACGGCTGGCAGTGGAAATCCCTGATCCGATTCAGAAGGGAGTGATTCAGCATAAAGAAAAATGC
AACCAA

Alignment

ORF - retro_sscr_171 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.44 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADEATRRVVSEIPVLKTNAGPRDRELWVQRLKEEYQSLIRYVENNKNADNDWFRLESNKEGTRWFGKCW
          MADEAT..V.SEI.VLK.N.G.RD.ELWVQRLKEE.Q.LI.Y.E.NKNADNDWF..E.NK.GTRW.GKCW
Retrocopy MADEATWHVTSEILVLKINTGSRDWELWVQRLKEEHQPLIWY-EKNKNADNDWF*PEPNKKGTRWSGKCW

Parental  YIHDLLKYEFDIEFDIPITYPTTAPEIAVPELDGKTAKMYRGGKICLTDHFKPLWARNVPKFGLAHLMAL
          YIHDLLKY....E.DIPITYPTTAPE.AVPELDGKTAKMY...KICL.DHF.PL.ARN.P.FGLAHL.A.
Retrocopy YIHDLLKY----ELDIPITYPTTAPESAVPELDGKTAKMYSDRKICLKDHFQPLCARNMPGFGLAHLLAM

Parental  GLGPWLAVEIPDLIQKGVIQHKEKCNQ
          GLGP.LAVEIPD.IQKGVIQHKEKCNQ
Retrocopy GLGPRLAVEIPDPIQKGVIQHKEKCNQ

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	24.16 RPM
SRP014902_testis	0.14 RPM	35.22 RPM
SRP018288_heart	0.03 RPM	40.21 RPM
SRP018288_kidney	0.00 RPM	83.53 RPM
SRP018288_liver	0.00 RPM	47.17 RPM
SRP018288_lung	0.00 RPM	41.04 RPM
SRP018856_adipose	0.12 RPM	63.50 RPM
SRP035408_brain	0.06 RPM	54.88 RPM
SRP035408_liver	0.00 RPM	52.72 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_171 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_171 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_171 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015545	1 retrocopy	retro_amel_1221,
Callithrix jacchus	ENSCJAG00000005303	3 retrocopies	retro_cjac_2546, retro_cjac_3146, retro_cjac_4122,
Danio rerio	ENSDARG00000022340	1 retrocopy	retro_drer_22,
Dasypus novemcinctus	ENSDNOG00000013733	1 retrocopy	retro_dnov_1943,
Echinops telfairi	ENSETEG00000015730	4 retrocopies	retro_etel_1042, retro_etel_562, retro_etel_714, retro_etel_83,
Felis catus	ENSFCAG00000009829	1 retrocopy	retro_fcat_1217,
Homo sapiens	ENSG00000143222	1 retrocopy	retro_hsap_3753,
Gorilla gorilla	ENSGGOG00000007486	1 retrocopy	retro_ggor_2525,
Loxodonta africana	ENSLAFG00000026969	1 retrocopy	retro_lafr_473,
Macropus eugenii	ENSMEUG00000004417	1 retrocopy	retro_meug_423,
Myotis lucifugus	ENSMLUG00000004543	1 retrocopy	retro_mluc_716,
Macaca mulatta	ENSMMUG00000022632	2 retrocopies	retro_mmul_1727, retro_mmul_2273,
Mustela putorius furo	ENSMPUG00000014243	1 retrocopy	retro_mputfur_854,
Nomascus leucogenys	ENSNLEG00000014049	1 retrocopy	retro_nleu_1893,
Oryctolagus cuniculus	ENSOCUG00000002389	1 retrocopy	retro_ocun_1304,
Otolemur garnettii	ENSOGAG00000026679	4 retrocopies	retro_ogar_1385, retro_ogar_2156, retro_ogar_3496, retro_ogar_496,
Ochotona princeps	ENSOPRG00000010906	3 retrocopies	retro_opri_319, retro_opri_509, retro_opri_773,
Pongo abelii	ENSPPYG00000000610	1 retrocopy	retro_pabe_3164,
Pan troglodytes	ENSPTRG00000001572	1 retrocopy	retro_ptro_2547,
Pteropus vampyrus	ENSPVAG00000005519	2 retrocopies	retro_pvam_1161, retro_pvam_814,
Sus scrofa	ENSSSCG00000006363	1 retrocopy	retro_sscr_171 ,
Tupaia belangeri	ENSTBEG00000016276	1 retrocopy	retro_tbel_2810,
Tarsius syrichta	ENSTSYG00000010824	1 retrocopy	retro_tsyr_1751,