RetrogeneDB ID: retro_sscr_681

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:120760155..120760730(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VDAC2
• Ensembl ID: ENSSSCG00000010320
• Aliases: None
• Description: voltage-dependent anion channel 2 [Source:HGNC Symbol;Acc:12672]

Sequence

>retro_sscr_681
ATTTCTCAAGGTTTGAAACTGATACTTGATAACACATTTTCACCGAACAATGGAAAGAAAAGTGGTAAAGTTAAGTCTTC
TTATAAAAGGGAGTATATAAACCTTGGTTGTGATGTTGACTTGTATTTTGCTGGACCTGCAATTCATGGTTCAGGGGTCT
TTGGTTATGAGGGCTTGCTTGCTGGGTACCAGTTGACCTTTGACAGTGCCTAATCAAAGCTCACAAACAGTAAGTCTGCA
GTGGGCTATGGGACTGGGGACTTCAAGCTGCACACTAATGTCATTGATAGGACAGAATTCAGAGGATCAATTTATCAAAA
AGTATGTGACGATCTTGACACATCAGTAAACCTTGCTTGGACATCCAGAACCAACTGCCCTTGCTTTGTATTGCAGCCAA
AGAGTTGGATCCCACTGTTTCCATTTCTGCAAAAGTCAACAATTCTAGTTTAAGTAGAGTGGGATATACTCAGACTCTGA
GGCCTGGTGTGAAGCTTCCATTATCTGTGCTGGTAGATGGGAAGAACATTCATGCTGGAGGGTACAAACTTGGGTTTTCC
CTGGAGTTGGAGGCT

Alignment

ORF - retro_sscr_681 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.21 %
• Parental protein coverage: 65.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ICQGLKLTFDTTFSPNTGKKSGKIKSSYKRECVNLGCDVDFDFAGPAIHGSAVFGYEGWVAYYDMRLDDC
          I.QGLKL..D.TFSPN.GKKSGK.KSSYKRE..NLGCDVD..FAGPAIHGS.VFGYEG..A.Y....D..
Retrocopy ISQGLKLILDNTFSPNNGKKSGKVKSSYKREYINLGCDVDLYFAGPAIHGSGVFGYEGLLAGYQLTFDSA

Parental  LKAKLNKNDALVNNRKRNFYFFYYSNDGTEFGGSIYQKVCEDLDTSVNLAWTSGTNCTRF-GIAAKYQLD
          ...KL......V......F.......D.TEF.GSIYQKVC.DLDTSVNLAWTS.TNC..F..IAAK..LD
Retrocopy -*SKLTNSKSAVGYGTGDFKLHTNVIDRTEFRGSIYQKVCDDLDTSVNLAWTSRTNCPCF<CIAAK-ELD

Parental  PTASISAKVNNSSLIGVGYTQTLRPGVKLTLSALVDGKSINAGGHKLGLALELEA
          PT.SISAKVNNSSL..VGYTQTLRPGVKL.LS.LVDGK.I.AGG.KLG..LELEA
Retrocopy PTVSISAKVNNSSLSRVGYTQTLRPGVKLPLSVLVDGKNIHAGGYKLGFSLELEA

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	101.01 RPM
SRP014902_testis	0.28 RPM	60.54 RPM
SRP018288_heart	0.00 RPM	296.96 RPM
SRP018288_kidney	0.00 RPM	173.86 RPM
SRP018288_liver	0.00 RPM	66.36 RPM
SRP018288_lung	0.00 RPM	88.28 RPM
SRP018856_adipose	0.00 RPM	115.61 RPM
SRP035408_brain	0.06 RPM	77.75 RPM
SRP035408_liver	0.00 RPM	53.99 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_681 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_681 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_681 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000013505	1 retrocopy	retro_rnor_2652,
Sus scrofa	ENSSSCG00000010320	2 retrocopies	retro_sscr_681 , retro_sscr_791,
Sus scrofa	ENSSSCG00000014296	2 retrocopies	retro_sscr_346, retro_sscr_801,
Tupaia belangeri	ENSTBEG00000001946	4 retrocopies	retro_tbel_1504, retro_tbel_1541, retro_tbel_1885, retro_tbel_4597,
Vicugna pacos	ENSVPAG00000008068	1 retrocopy	retro_vpac_156,