RetrogeneDB ID: retro_sscr_955

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:119831154..119831326(-)
• Located in intron of: ENSSSCG00000002442

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000013863
• Aliases: None
• Description: None

Sequence

>retro_sscr_955
CTGTTCAGGACGCTGCTGATGACCGCTGGGGGCAGTGCTCAACTTGAAGCTGAAAAGAAAGGGCACTCAGGGCTTTGGGA
AGGAGCCGAGGGAACCCAGCACAGGTGATACCAGCCTTATGCTCTTACTGAGCCTTAGACACGTCAGAATCTCATTACCC
TGGGGAACTTTT

Alignment

ORF - retro_sscr_955 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.41 %
• Parental protein coverage: 77.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LFGTLLMNAG-AVLNFKLKKKDTQGFGEESREPSTGDNIREFLLSLRYFRIFIALWNVF
          LF.TLLM.AG.AVLN.KLK.K.TQGFG.E.REPSTGD.....LLSLR..RI....W..F
Retrocopy LFRTLLMTAG>AVLNLKLKRKGTQGFGKEPREPSTGDTSLMLLLSLRHVRISLP-WGTF

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	6.11 RPM
SRP014902_testis	0.00 RPM	18.25 RPM
SRP018288_heart	0.00 RPM	24.70 RPM
SRP018288_kidney	0.00 RPM	26.10 RPM
SRP018288_liver	0.00 RPM	11.35 RPM
SRP018288_lung	0.00 RPM	11.00 RPM
SRP018856_adipose	0.00 RPM	156.04 RPM
SRP035408_brain	0.00 RPM	4.45 RPM
SRP035408_liver	0.00 RPM	3.29 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_955 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_955 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_955 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_1927
Equus caballus	retro_ecab_640

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010105	1 retrocopy	retro_amel_1688,
Canis familiaris	ENSCAFG00000015643	1 retrocopy	retro_cfam_1927,
Callithrix jacchus	ENSCJAG00000013936	1 retrocopy	retro_cjac_1223,
Equus caballus	ENSECAG00000026861	1 retrocopy	retro_ecab_640,
Felis catus	ENSFCAG00000016411	1 retrocopy	retro_fcat_934,
Homo sapiens	ENSG00000214046	1 retrocopy	retro_hsap_2244,
Mus musculus	ENSMUSG00000044600	1 retrocopy	retro_mmus_450,
Nomascus leucogenys	ENSNLEG00000005569	1 retrocopy	retro_nleu_1315,
Pongo abelii	ENSPPYG00000009694	2 retrocopies	retro_pabe_1964, retro_pabe_2031,
Pan troglodytes	ENSPTRG00000010650	1 retrocopy	retro_ptro_1589,
Rattus norvegicus	ENSRNOG00000042037	1 retrocopy	retro_rnor_2694,
Sus scrofa	ENSSSCG00000013863	1 retrocopy	retro_sscr_955 ,
Tarsius syrichta	ENSTSYG00000009556	1 retrocopy	retro_tsyr_1550,
Tursiops truncatus	ENSTTRG00000015020	2 retrocopies	retro_ttru_136, retro_ttru_597,
Vicugna pacos	ENSVPAG00000006699	1 retrocopy	retro_vpac_65,