RetrogeneDB ID: retro_sscr_652

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:149170947..149171610(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000023126
• Aliases: None
• Description: None

Sequence

>retro_sscr_652
ATGTCTGAATATACTGGGGTAAGAGAAGATAAGAATGGTGAGCTCCTTGAAGTACTATCAGAAGAGGATCGACCGTGCTG
TGGCCCACAGTTACAGCCCAGGTTTTCAGGGGTGTGGGGGCTGCCCTGCAGAAATCCAGTGTCTCAGTATACGAGAGGCG
TCTACCTGGTCGAAGGAATTCCGCATGCCCCTCATGCTGGCTACGGGAATCTGGTGTATGTTGTCAACTATCCTAAAGAC
AACAAAAGAAGAATGGATGGGACAGATCCTTCATCAGCTGTGACAGTGAAAAGAGAAGTCCAGACAACATCTGATGTAAT
AGTGTTGGGTCGCCCATGGAAAACAACCGAACAGGATCTAAAAGCATATTTTAGTACCTTTGGAAAGGTGCTTAGGGTTC
AAGTCAAGAAAAATGTTAAAACTCATCACTCAAAGGGGTTTGGCTTTGTTCATTTTGTGGAATATGAAACCCAGGTGAAA
GTCATATCACAGCGACATATGGTGGAGAGACAATGGTGTGACTGTAACCTTTGAAATTCTAAGCAAAGCCCAGATGAGCC
TTTGCGAAGCAGAAGGGTGTTGGTTGGACATTGTGCAGAGGACATGACTGCTGATGCGTTACAGCAGTGGTGGCTGTCTT
CATTCCAAGCCATTCAGGGCTTT

Alignment

ORF - retro_sscr_652 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.4 %
• Parental protein coverage: 53.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSEYIRVT-DENDEPIEIPSEDD-GTVLLSTVTAQ-FPGACGLRYRNPVSQCMRGVRLVEGILHAPDAGW
          MSEY..V..D.N.E..E..SE.D..TVL..TVTAQ.F.G..GL..RNPVSQ..RGV.LVEGI.HAP.AG.
Retrocopy MSEYTGVREDKNGELLEVLSEED<STVLWPTVTAQ>FSGVWGLPCRNPVSQYTRGVYLVEGIPHAPHAGY

Parental  GNLVYVVNYPKDNKRKMDETDASSAVKVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKD
          GNLVYVVNYPKDNKR.MD.TD.SSAV.VKR.VQ.TSD.IVLG.PWKTTEQDLK.YFSTFG.VL.VQVKK.
Retrocopy GNLVYVVNYPKDNKRRMDGTDPSSAVTVKREVQTTSDVIVLGRPWKTTEQDLKAYFSTFGKVLRVQVKKN

Parental  IKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQSPDEPLRSRKVFVGRCTEDMTADELQ
          .KT.HSKGFGFV.F.EYETQVKV.SQRHM....WCDC.L.NSKQSPDEPLRSR.V.VG.C.EDMTAD.LQ
Retrocopy VKTHHSKGFGFVHFVEYETQVKVISQRHMVERQWCDCNL*NSKQSPDEPLRSRRVLVGHCAEDMTADALQ

Parental  QFFCQYGEVVDVF
          Q...........F
Retrocopy QWWLSSFQAIQGF

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	9.95 RPM
SRP014902_testis	0.00 RPM	37.62 RPM
SRP018288_heart	0.03 RPM	29.83 RPM
SRP018288_kidney	0.00 RPM	44.92 RPM
SRP018288_liver	0.00 RPM	23.51 RPM
SRP018288_lung	0.00 RPM	41.44 RPM
SRP018856_adipose	0.14 RPM	96.77 RPM
SRP035408_brain	0.00 RPM	16.20 RPM
SRP035408_liver	0.00 RPM	17.20 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_sscr_652 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
EW612694	149171074	149171177	100	103	0	103

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_652 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_652 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002381	2 retrocopies	retro_cjac_2457, retro_cjac_525,
Dasypus novemcinctus	ENSDNOG00000008531	1 retrocopy	retro_dnov_2262,
Homo sapiens	ENSG00000120948	2 retrocopies	retro_hsap_1209, retro_hsap_3637,
Macaca mulatta	ENSMMUG00000007456	1 retrocopy	retro_mmul_1847,
Mus musculus	ENSMUSG00000041459	1 retrocopy	retro_mmus_1958,
Nomascus leucogenys	ENSNLEG00000009512	2 retrocopies	retro_nleu_201, retro_nleu_819,
Pongo abelii	ENSPPYG00000001894	1 retrocopy	retro_pabe_1008,
Pan troglodytes	ENSPTRG00000000136	2 retrocopies	retro_ptro_2460, retro_ptro_828,
Sus scrofa	ENSSSCG00000023126	1 retrocopy	retro_sscr_652 ,
Tarsius syrichta	ENSTSYG00000004077	1 retrocopy	retro_tsyr_2004,
Drosophila melanogaster	FBgn0025790	1 retrocopy	retro_dmel_17,