RetrogeneDB ID: retro_sscr_520

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 16:29671803..29672087(+)
• Located in intron of: ENSSSCG00000029546

Retrocopy information

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

Parental gene information

• Parental gene symbol: NRAS
• Ensembl ID: ENSSSCG00000006753
• Aliases: NRAS, H-RAS, HRAS
• Description: Sus scrofa neuroblastoma RAS viral (v-ras) oncogene homolog (NRAS), mRNA. [Source:RefSeq mRNA;Acc:NM_001044537]

Sequence

>retro_sscr_520
GGTGGTGGGAAAAGCACAATGACAATCCCACTGATCCAGAACCACTTTGTAGATAAATATGATCCCACCACAGAGAATCT
TACCCAAAACAGATGGTTATACGTGGTGAAGCCTGTCTGCTGGACATACCAGATACAGCTGGACAAGAGGAGCACAGTGC
CAAGAGAGACCAATACATGAGGACAGATGAAGGCTTGCCTTGAGTATTTGCAATCAATAAAGGCAAATCATTTGCACATA
TTAACCCCTACAGGGGAGAGATTTAGCACATAAAAGACTCAGAT

Alignment

ORF - retro_sscr_520 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.83 %
• Parental protein coverage: 50.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GVGKSALTIQLIQNHFVDEYDPTIE-DSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCV
          G.GKS..TI.LIQNHFVD.YDPT.E..SY.KQ.VI.GE.CLLDI.DTAGQEE.SA.RDQYMRT.EG...V
Retrocopy GGGKSTMTIPLIQNHFVDKYDPTTE<ESYPKQMVIRGEACLLDIPDTAGQEEHSAKRDQYMRTDEGLP*V

Parental  FAINNSKSFADINLYREQIKRVKDSD
          FAIN..KSFA.IN.YR..I...KDSD
Retrocopy FAINKGKSFAHINPYRGEI*HIKDSD

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	16.72 RPM
SRP014902_testis	0.00 RPM	23.34 RPM
SRP018288_heart	0.00 RPM	12.02 RPM
SRP018288_kidney	0.10 RPM	29.95 RPM
SRP018288_liver	0.16 RPM	12.15 RPM
SRP018288_lung	0.00 RPM	27.09 RPM
SRP018856_adipose	0.00 RPM	32.62 RPM
SRP035408_brain	0.00 RPM	11.75 RPM
SRP035408_liver	0.00 RPM	16.64 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_520 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_520 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_520 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017134	1 retrocopy	retro_amel_885,
Callithrix jacchus	ENSCJAG00000036517	1 retrocopy	retro_cjac_2400,
Felis catus	ENSFCAG00000019026	1 retrocopy	retro_fcat_1191,
Loxodonta africana	ENSLAFG00000020706	1 retrocopy	retro_lafr_492,
Macropus eugenii	ENSMEUG00000002675	1 retrocopy	retro_meug_2136,
Myotis lucifugus	ENSMLUG00000022354	1 retrocopy	retro_mluc_741,
Monodelphis domestica	ENSMODG00000004590	1 retrocopy	retro_mdom_51,
Oryctolagus cuniculus	ENSOCUG00000022455	1 retrocopy	retro_ocun_850,
Rattus norvegicus	ENSRNOG00000023079	2 retrocopies	retro_rnor_2867, retro_rnor_619,
Sus scrofa	ENSSSCG00000006753	1 retrocopy	retro_sscr_520 ,
Sus scrofa	ENSSSCG00000021148	1 retrocopy	retro_sscr_1125,
Sus scrofa	ENSSSCG00000029741	1 retrocopy	retro_sscr_634,
Sus scrofa	ENSSSCG00000030014	2 retrocopies	retro_sscr_435, retro_sscr_909,