RetrogeneDB ID: retro_sscr_958

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:131119929..131120166(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPF
• Ensembl ID: ENSSSCG00000000895
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptide F [Source:HGNC Symbol;Acc:11162]

Sequence

>retro_sscr_958
CTCAGTCCTGGCCCTTTCCTCAGTGGAGTCACAGGAAGGCCAGTCATGGTGAAACTGGAGTGGGGAATGGAGTACGGAGG
CTACCTGGTATCTGTCGGTGGCTCTCAGAACAGGCAGCTTGCAAGCACAGAAGAACACAGAGGGAGCGTTGTCTGGGCAT
TTGGGTGAAGCTTAATAAGGTGTAAGAATGGCGTTTATATCAAGGGTATTGGAGAAGACGATGGGGAAATGAGAGAA

Alignment

ORF - retro_sscr_958 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.98 %
• Parental protein coverage: 95.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLYIRG
          L.P.PFL.G.TG.PVMVKL.WGMEY.GYLVSV.G..N.QLA.TEE...G......G..LIRC.N..YI.G
Retrocopy LSPGPFLSGVTGRPVMVKLEWGMEYGGYLVSVGGSQNRQLASTEEH-RGSVVWAFG*SLIRCKNGVYIKG

Parental  VEEEEEDGEMRE
          ....E.DGEMRE
Retrocopy I--GEDDGEMRE

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	0.13 RPM	18.05 RPM
SRP014902_testis	0.00 RPM	40.74 RPM
SRP018288_heart	0.00 RPM	14.75 RPM
SRP018288_kidney	0.00 RPM	15.56 RPM
SRP018288_liver	0.48 RPM	11.35 RPM
SRP018288_lung	0.00 RPM	23.32 RPM
SRP018856_adipose	0.00 RPM	15.29 RPM
SRP035408_brain	0.00 RPM	66.09 RPM
SRP035408_liver	0.12 RPM	59.50 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_958 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_958 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_958 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002166	3 retrocopies	retro_amel_1239, retro_amel_42, retro_amel_883,
Bos taurus	ENSBTAG00000016271	1 retrocopy	retro_btau_765,
Equus caballus	ENSECAG00000019817	1 retrocopy	retro_ecab_154,
Felis catus	ENSFCAG00000029966	4 retrocopies	retro_fcat_280, retro_fcat_66, retro_fcat_77, retro_fcat_861,
Homo sapiens	ENSG00000139343	3 retrocopies	retro_hsap_125, retro_hsap_2487, retro_hsap_2645,
Gorilla gorilla	ENSGGOG00000001127	2 retrocopies	retro_ggor_1549, retro_ggor_225,
Macaca mulatta	ENSMMUG00000009302	4 retrocopies	retro_mmul_1521, retro_mmul_361, retro_mmul_550, retro_mmul_893,
Mustela putorius furo	ENSMPUG00000007176	3 retrocopies	retro_mputfur_1309, retro_mputfur_377, retro_mputfur_941,
Mus musculus	ENSMUSG00000020018	4 retrocopies	retro_mmus_1060, retro_mmus_1197, retro_mmus_2537, retro_mmus_3210,
Nomascus leucogenys	ENSNLEG00000005835	3 retrocopies	retro_nleu_2259, retro_nleu_274, retro_nleu_651,
Pongo abelii	ENSPPYG00000004847	2 retrocopies	retro_pabe_381, retro_pabe_489,
Pteropus vampyrus	ENSPVAG00000009036	1 retrocopy	retro_pvam_1170,
Rattus norvegicus	ENSRNOG00000005556	4 retrocopies	retro_rnor_1822, retro_rnor_1849, retro_rnor_2926, retro_rnor_444,
Sus scrofa	ENSSSCG00000000895	1 retrocopy	retro_sscr_958 ,
Sus scrofa	ENSSSCG00000009036	2 retrocopies	retro_sscr_474, retro_sscr_475,