RetrogeneDB ID: retro_sscr_130

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:195103854..195104157(+)
• Located in intron of: ENSSSCG00000027765

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000026046
• Aliases: None
• Description: None

Sequence

>retro_sscr_130
AGCTTTCCCAGGCCAGCGCACAGGCATATGGGCTAGAGCACCTTCAATGAAGTATAGGACCTCTCCGAGGACAGGTTTCT
GCTGCTGGCTGTGCTCCAGGGGGTGGCTGCCGAACTCACAAGAGTGGAAATATGCCTAGAAGTAGGGTCAGGGTCTGAAG
TGGTATCTGCATTGTGAGCCTGTATGATAGGTCCTCAAGCTTTGTACATGTGTACTGATGTCAACCCTGAGGCAGCAGCC
TATACCCTGGAGAACGCATGCTGTAACAAAGTCCACATTCAACCAATAATTACAGATTTGGTC

Alignment

ORF - retro_sscr_130 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.31 %
• Parental protein coverage: 92.66 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SFPTPEYGHVGRGVFSDVYEPAEDTFLLLDALEAAAAEFSGVEICLEVGSGSGVVSAFLASVIGPQALYM
          SFP.P...H.G...F..V....ED.FLLL..L...AAE...VEICLEVGSGS.VVSA..A..IGPQALYM
Retrocopy SFPRPAHRHMG*STFNEV*DLSEDRFLLLAVLQGVAAELTRVEICLEVGSGSEVVSAL*ACMIGPQALYM

Parental  CTDVNPEAAACTLETARCNKVHIQPIITDLV
          CTDVNPEAAA.TLE.A.CNKVHIQPIITDLV
Retrocopy CTDVNPEAAAYTLENACCNKVHIQPIITDLV

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	1.33 RPM
SRP014902_testis	0.00 RPM	4.95 RPM
SRP018288_heart	0.00 RPM	1.28 RPM
SRP018288_kidney	0.00 RPM	1.87 RPM
SRP018288_liver	0.16 RPM	1.12 RPM
SRP018288_lung	0.10 RPM	2.34 RPM
SRP018856_adipose	0.00 RPM	5.71 RPM
SRP035408_brain	0.00 RPM	0.32 RPM
SRP035408_liver	0.00 RPM	0.68 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_130 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_130 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_130 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005227	1 retrocopy	retro_chof_1139,
Homo sapiens	ENSG00000156239	1 retrocopy	retro_hsap_916,
Gorilla gorilla	ENSGGOG00000022382	1 retrocopy	retro_ggor_739,
Nomascus leucogenys	ENSNLEG00000002845	1 retrocopy	retro_nleu_282,
Oryctolagus cuniculus	ENSOCUG00000001084	1 retrocopy	retro_ocun_521,
Ochotona princeps	ENSOPRG00000001551	3 retrocopies	retro_opri_200, retro_opri_867, retro_opri_925,
Pongo abelii	ENSPPYG00000011314	1 retrocopy	retro_pabe_790,
Pan troglodytes	ENSPTRG00000013817	1 retrocopy	retro_ptro_635,
Pteropus vampyrus	ENSPVAG00000012777	2 retrocopies	retro_pvam_1166, retro_pvam_1200,
Sus scrofa	ENSSSCG00000026046	1 retrocopy	retro_sscr_130 ,
Ictidomys tridecemlineatus	ENSSTOG00000021743	1 retrocopy	retro_itri_497,
Tupaia belangeri	ENSTBEG00000001269	1 retrocopy	retro_tbel_777,