RetrogeneDB ID: retro_sscr_597

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 18:26128659..26129394(+)
• Located in intron of: ENSSSCG00000016611

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF128
• Ensembl ID: ENSSSCG00000012551
• Aliases: None
• Description: ring finger protein 128, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:21153]

Sequence

>retro_sscr_597
ACGTGGCTCGCACTGGTTGAACGGGGAGGTTGCACCTTCACACAGAAGATCAAGGTGGCCGTGGAAAAGGGAGCCAGTGG
AGTCATCATCTACAACTTCCCAGGAACTGGCAATCAGGTCTTTCCCATGTCTCATCAGACCTTCGAAGACATCGTTGTGG
TCATGATTGGTAACTTAAAAGGCATGGAGATTTTGCATTTAATTCGGAAGGGAGTTCACGTCACAGTCATGATTGAGGTG
GGAAGAAAACACATCATCTGGATGAATCACTATTTTGTCTCTTTTGTGATCGTCACAACTGCTACTTTAGCATATTTCAT
CTTTTATCATATTCGAAGACTTTGGGTAGCAAGGATTCAGAGCAGAAGATGGCAGCGGTTAACTACCGATCTCAAGAAAG
CCTTCGGCCAACTTCAACTTCGGGTCCTGAAAGAGGGAGACGACGAGGTCGGTCCCAATGGCGATAGCTGTGTGGTTTGC
TTTGAACTCTATAAGCCTAATGATACCGTTCGTATTCTGACTTGTAAACACTTTTTCCACAAGAATTGCATTGACCCCTG
GGTTCTAGCCCACGGGACGTGCCCCATGTGCAAATGTGACATTCTTAAAGCTCTGGGGATTCAAGTGGATGTTGAAGATG
GAACAGAATCTTTGCAAATCCTAATGTCGAGTGAACTGCCTGGTCTCTTGTCACCTAGTGAGGAAGGCCCTGGTAATGAA
CCTCCTCCTGCAGGA

Alignment

ORF - retro_sscr_597 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.57 %
• Parental protein coverage: 58.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SWLALIQRGGGCTFADKIHLAYERGASGAVIFNFPGTRNEVIPMSHPGAGDIVAIMIGNLKGTKILQSIQ
          .WLAL..RGG.CTF..KI..A.E.GASG..I.NFPGT.N.V.PMSH....DIV..MIGNLKG..IL..I.
Retrocopy TWLALVERGG-CTFTQKIKVAVEKGASGVIIYNFPGTGNQVFPMSHQTFEDIVVVMIGNLKGMEILHLIR

Parental  RGIQVTMVIEVGKKHGPWVNHYSIFFVSVSFFIITAATVGYFIFYSARRLRNARAQSRKQRQLKADAKKA
          .G..VT..IEVG.KH..W.NHY...FV.V.....TA...........RRL..AR.QSR....L..D.KKA
Retrocopy KGVHVTVMIEVGRKHIIWMNHYFVSFVIVT----TATLAYFIFYH-IRRLWVARIQSRRWQRLTTDLKKA

Parental  IGRLQLRTLKQGDKEIGPDGDSCAVCIELYKPNDLVRILTCNHIFHKTCVDPWLLEHRTCPMCKCDILKA
          .G.LQLR.LK.GD.E.GP.GDSC.VC.ELYKPND.VRILTC.H.FHK.C.DPW.L.H.TCPMCKCDILKA
Retrocopy FGQLQLRVLKEGDDEVGPNGDSCVVCFELYKPNDTVRILTCKHFFHKNCIDPWVLAHGTCPMCKCDILKA

Parental  LGIEVDVEDGSVSLQVPVSNETSNSASPHEEDNRSETASSG
          LGI.VDVEDG..SLQ...S.E.....SP.EE....E....G
Retrocopy LGIQVDVEDGTESLQILMSSELPGLLSPSEEGPGNEPPPAG

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	5.44 RPM
SRP014902_testis	0.00 RPM	25.88 RPM
SRP018288_heart	0.00 RPM	53.93 RPM
SRP018288_kidney	0.10 RPM	257.40 RPM
SRP018288_liver	0.00 RPM	85.71 RPM
SRP018288_lung	0.10 RPM	14.66 RPM
SRP018856_adipose	0.00 RPM	0.28 RPM
SRP035408_brain	0.00 RPM	76.48 RPM
SRP035408_liver	0.06 RPM	468.81 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_597 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_597 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_597 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2651
Oryctolagus cuniculus	retro_ocun_37
Bos taurus	retro_btau_1358

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000022920	1 retrocopy	retro_btau_1358,
Loxodonta africana	ENSLAFG00000002816	1 retrocopy	retro_lafr_946,
Macropus eugenii	ENSMEUG00000001567	1 retrocopy	retro_meug_1139,
Mustela putorius furo	ENSMPUG00000003695	1 retrocopy	retro_mputfur_340,
Oryctolagus cuniculus	ENSOCUG00000012328	1 retrocopy	retro_ocun_37,
Pelodiscus sinensis	ENSPSIG00000010727	1 retrocopy	retro_psin_49,
Pan troglodytes	ENSPTRG00000022151	1 retrocopy	retro_ptro_2651,
Sus scrofa	ENSSSCG00000012551	1 retrocopy	retro_sscr_597 ,
Sus scrofa	ENSSSCG00000014013	3 retrocopies	retro_sscr_150, retro_sscr_253, retro_sscr_254,
Sus scrofa	ENSSSCG00000017906	1 retrocopy	retro_sscr_518,
Ictidomys tridecemlineatus	ENSSTOG00000022922	2 retrocopies	retro_itri_1254, retro_itri_1255,
Tursiops truncatus	ENSTTRG00000007536	1 retrocopy	retro_ttru_6,