RetrogeneDB ID: retro_sscr_144

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:282978451..282979260(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDRG3
• Ensembl ID: ENSSSCG00000007322
• Aliases: None
• Description: NDRG family member 3 [Source:HGNC Symbol;Acc:14462]

Sequence

>retro_sscr_144
ATGGATGAACTTCAGAATGTTCAACTCACATAGATCAAATCACTTCTAAATGATAAGAATAGTACACAAAACTTCCAGAA
CTTTGACCGTCAGGAACATGATACAGAAACAACATATGGTATGGTTCATGTCACTATAAGAAGCCTACCGAAGGGAAAAA
GACCAGTTATTATAACATACCATGACATTGGTCTCAATTATAAATCCTGTTTCAATATATTCTTTAACTTTGAGGATATG
CAAGAAATCACTCAGCACTTTGCTGTCTGAACCATGGACTCCTCGGGCCAGCAGGAAGTTGCATCCTCTTCCCCAACTGG
GTACCAGTACCCCACACTGGATGAGCTAGCCAAATGCTGCCTTCTGTTCTCAACCACTTAAATCTAAATAGATTTAGTGT
TGGAGCTGGAGCTAGAGCTTCTATTCTCAGCAGATTTGCAGTCAATCACCCAGAGTTTGTGGGAGGTCTTGTACTCATTA
ATGTTGGCTCTTGTGCTAAAGGCTGGATTGACGGGGCAGCTTTCAAACTCTCAGGATTGACAATCGATGTTGTGGACATT
ATTTTGGCTCATCACTTTGGGCAGGAAGAGTTGCAGGCCAACCTGGACCTGATTCAAACCTACAGACTGCATATTACCCA
AGGTATCAACCAATAAAACCTACACCTCTTCCTGAGTTCTTATAACAAATGCAAAGACCTAGAGATTGAAAGACGCATCC
TGAGACAAAATGATAACAAATCAAAGACATTAAAGTGTTCTGCTTTATTGGTGGTAGGCAACAATTCACCCCCAGTTGAG
GCTATGGTT

Alignment

ORF - retro_sscr_144 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.04 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDELQDVQLTEIKPLLNDKNGTRNFQDFDCQEHDIETTHGVVHVTIRGLPKGNRPVIMTYHDIGLNHKSC
          MDELQ.VQLT.IK.LLNDKN.T.NFQ.FD.QEHD.ETT.G.VHVTIR.LPKG.RPVI.TYHDIGLN.KSC
Retrocopy MDELQNVQLT*IKSLLNDKNSTQNFQNFDRQEHDTETTYGMVHVTIRSLPKGKRPVIITYHDIGLNYKSC

Parental  FNAFFNFEDMQEITQHFAVCHVDAPGQQEGAPSFPSGYQYPTMDELA-EMLPSVLTHLNLKSIIGVGVGA
          FN.FFNFEDMQEITQHFAV...D..GQQE.A.S.P.GYQYPT.DELA..MLPSVL.HLNL.....VG.GA
Retrocopy FNIFFNFEDMQEITQHFAV*TMDSSGQQEVASSSPTGYQYPTLDELA<QMLPSVLNHLNLNRF-SVGAGA

Parental  GAYILSRFALNHPELVEGLVLINVDPCAKGWIDWAASKLSGLTTNVVDIILAHHFGQEELQANLDLIQTY
          .A.ILSRFA.NHPE.V.GLVLINV..CAKGWID.AA.KLSGLT..VVDIILAHHFGQEELQANLDLIQTY
Retrocopy RASILSRFAVNHPEFVGGLVLINVGSCAKGWIDGAAFKLSGLTIDVVDIILAHHFGQEELQANLDLIQTY

Parental  RLHIAQDINQENLQLFLSSYNGRKDLEIERPILGQNDNKSKTLKCSTLLVVGDNSPAVEAVV
          RLHI.Q.INQ.NL.LFLSSYN..KDLEIER.IL.QNDNKSKTLKCS.LLVVG.NSP.VEA.V
Retrocopy RLHITQGINQ*NLHLFLSSYNKCKDLEIERRILRQNDNKSKTLKCSALLVVGNNSPPVEAMV

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	4.38 RPM
SRP014902_testis	0.00 RPM	10.61 RPM
SRP018288_heart	0.00 RPM	5.24 RPM
SRP018288_kidney	0.00 RPM	17.93 RPM
SRP018288_liver	0.00 RPM	2.40 RPM
SRP018288_lung	0.00 RPM	10.49 RPM
SRP018856_adipose	0.00 RPM	7.74 RPM
SRP035408_brain	0.00 RPM	33.92 RPM
SRP035408_liver	0.00 RPM	2.03 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_144 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_144 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_144 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012562	1 retrocopy	retro_amel_378,
Echinops telfairi	ENSETEG00000002250	1 retrocopy	retro_etel_2102,
Myotis lucifugus	ENSMLUG00000009735	1 retrocopy	retro_mluc_1054,
Otolemur garnettii	ENSOGAG00000000895	1 retrocopy	retro_ogar_515,
Sus scrofa	ENSSSCG00000007322	5 retrocopies	retro_sscr_1116, retro_sscr_144 , retro_sscr_519, retro_sscr_539, retro_sscr_937,
Ictidomys tridecemlineatus	ENSSTOG00000022531	1 retrocopy	retro_itri_1284,