RetrogeneDB ID: retro_sscr_1076

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 9:144313708..144314257(-)
• Located in intron of: ENSSSCG00000015600

Retrocopy information

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

Parental gene information

• Parental gene symbol: NME6
• Ensembl ID: ENSSSCG00000011347
• Aliases: None
• Description: NME/NM23 nucleoside diphosphate kinase 6 [Source:HGNC Symbol;Acc:20567]

Sequence

>retro_sscr_1076
ATGACTTCTACCTTACCGAGCCCCGGGCTGTCCAGCTCACTCTGGAACTGATCACGCCTCATGCAGTTGCTCATCCACTG
ATTCTGGAAGCTATTAATCAGCAGGTTCTGAGCAACAAGTTCGTTATTGTAAGAATGAGAGCACGTCTTTTGAGAAGGGA
AGATTGCCAGAAGTTTTCCCAAGGGCAGGAAGGGTATATTTTTCTATCAGTGGCTGGTGGTATTCATGGCCCATGGGCTG
ATCCAAGCCTGTACCCTCGCCCGCAAGGATGTCATCAGCTCTGGAGGACAGTGATGGGACTCACCAGAATGTTCTGAGCT
CGCCACGTAGCCCCAGATTCAATTTGTGGGAGTTTCGGCCTCACTGACACCCACGGTACAACCCATGGCTCTGACTCTGG
TTTCGGCCAGTAGAGAGACTGCAGCCTTTTCCCCTGACTTCAGCGGACAGCACTGGGATGAGGAAGAAGAGCCCCAGTTG
CGCTGTGGGCCTGTGCACTACAGTCCGGAAGGAGGTGTGCACTGTGCAGCTGGAACAGAAGGCCCAGGG

Alignment

ORF - retro_sscr_1076 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.81 %
• Parental protein coverage: 98.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MTSILRSP-QALQLTLALIKPDAVAHPLILEAIHQQILSNKFLIVRMRELLWRKEDCQKFYQEHEGR-FF
          MTS.L.SP..A.QLTL.LI.P.AVAHPLILEAI.QQ.LSNKF.IVRMR..L.R.EDCQKF.Q..EG..FF
Retrocopy MTSTLPSP<RAVQLTLELITPHAVAHPLILEAINQQVLSNKFVIVRMRARLLRREDCQKFSQGQEGY>FF

Parental  YQRLVEFMASGPIRAYILAHKDAI-QLWRTVMGPTRVFRARHIAPDSIRGSFGLTDTRNTTHGSDSVVSA
          YQ.LV.FMA.G.I.A..LA.KD.I.QLWRTVMG.TR.F.ARH.APDSI.GSFGLTDT..TTHGSDS....
Retrocopy YQWLVVFMAHGLIQACTLARKDVI<QLWRTVMGLTRMF*ARHVAPDSICGSFGLTDTHGTTHGSDSGFGQ

Parental  SREIAAFFP-DFSEQRWYEEEEPQLRCGPVHYSPEGGIHCAAGTGGPG
          .R.....FP.DFS.Q.W.EEEEPQLRCGPVHYSPEGG.HCAAGT.GPG
Retrocopy *RD-CSLFP>DFSGQHWDEEEEPQLRCGPVHYSPEGGVHCAAGTEGPG

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	20.71 RPM
SRP014902_testis	0.00 RPM	19.24 RPM
SRP018288_heart	0.00 RPM	7.78 RPM
SRP018288_kidney	0.00 RPM	22.95 RPM
SRP018288_liver	0.00 RPM	20.47 RPM
SRP018288_lung	0.00 RPM	12.93 RPM
SRP018856_adipose	0.00 RPM	33.83 RPM
SRP035408_brain	0.00 RPM	7.72 RPM
SRP035408_liver	0.00 RPM	36.67 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1076 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1076 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1076 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000032478	1 retrocopy	retro_mmus_2376,
Sus scrofa	ENSSSCG00000007986	2 retrocopies	retro_sscr_1113, retro_sscr_852,
Sus scrofa	ENSSSCG00000011347	1 retrocopy	retro_sscr_1076 ,
Sus scrofa	ENSSSCG00000017591	1 retrocopy	retro_sscr_854,
Ictidomys tridecemlineatus	ENSSTOG00000002690	1 retrocopy	retro_itri_675,