RetrogeneDB ID: retro_sscr_791

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 5:19088320..19089146(+)
• 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_791
TTTGCTGACCTTGGCAAAGCTGCCAGAGATATTTTCAATAAAGGATTTGGTTTGGGGGTTGGTGAAACTGGCTGTGAGAA
CAAAGTCATGCGGTGGCATGGAATTCTTAACACGTGGTTCATCTAACCCATTCACTGGGTAAAGTTGCTGGGACCTTGGA
GACCAAATATGAATGGTGTGAGCATGGTCTGACTTTCACTGAGAAGTGGAACACTGATAATGCTCTTGGAACAGAAATCG
CTATTGAAGACCAGATTTGTCAAGGTTTGAAACTGACATTTGATTCTACCTTTTCAGCAAGCACAGGAAAGAAAAGTGGT
AAAATCGAGTCTTCTCACAAGAGGGAGTGTATAAACCTTGGTTGGGATGTTGACTTTGCTGAACCTGCAATCTGTGGTTC
AGCTGTCTTTGGTCATGAGGGCTGGCTTGCTGGGCACCAGATGACCCTTGCCAGGGCCGAAGCAAAGCTGACAAGGAATA
ACTTTGCAGTGGGCTACAGGACTGGGGACTACCAGCTACACACTAATGTCAAGGATGGGACAGCATTTGGAGGATCGATT
TATCAGAAATACGTGGAGATCTTGACACTTCAGTAAACCTTTCTTGGACATCAGGGACCAACGGCACTAGCTTTGGCATT
GCAGCTAAATATCAGTTGGATCCCACTACTTCCATTTCTGCAAAAGTCAACAACTCTAGTTAAATTGGAGTGGGCTGCAC
TCAGACCCTGAGGCCTGCTGTGAAGCTGTCACTGTCTGCTGTGGTAGATGGGAAGAGCATTAATGCTGGAAGCCACAAAC
TTGGGCTTGCCCTGGAGCTGGAAGCT

Alignment

ORF - retro_sscr_791 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.09 %
• Parental protein coverage: 94.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YADLGKAARDIFNKGFG-FGLVKLDVKTKSCSGVEFSTSGSSNTDTG-KVTGTLETKYKWCEYGLTFTEK
          .ADLGKAARDIFNKGFG..GLVKL.V.TKSC.G.EF.T.GSSN..TG.KV.GTLETKY.WCE.GLTFTEK
Retrocopy FADLGKAARDIFNKGFG>WGLVKLAVRTKSCGGMEFLTRGSSNPFTG>KVAGTLETKYEWCEHGLTFTEK

Parental  WNTDNTLGTEIAIEDQICQGLKLTFDTTFSPNTGKKSGKIKSSYKRECVNLGCDVDFDFAGPAIHGSAVF
          WNTDN.LGTEIAIEDQICQGLKLTFD.TFS..TGKKSGKI.SS.KREC.NLG.DV..DFA.PAI.GSAVF
Retrocopy WNTDNALGTEIAIEDQICQGLKLTFDSTFSASTGKKSGKIESSHKRECINLGWDV--DFAEPAICGSAVF

Parental  GYEGWVAYYDMRLDDCLKAKLNKNDALVNNRKRNFYFFYYSNDGTEFGGSIYQKVCE-DLDTSVNLAWTS
          G.EGW.A...M.L.....AKL..N...V..R...........DGT.FGGSIYQK..E.DLDTSVNL.WTS
Retrocopy GHEGWLAGHQMTLARA-EAKLTRNNFAVGYRTGDYQLHTNVKDGTAFGGSIYQKYVE<DLDTSVNLSWTS

Parental  GTNCTRFGIAAKYQLDPTASISAKVNNSSLIGVGYTQTLRPGVKLTLSALVDGKSINAGGHKLGLALELE
          GTN.T.FGIAAKYQLDPT.SISAKVNNSS.IGVG.TQTLRP.VKL.LSA.VDGKSINAG.HKLGLALELE
Retrocopy GTNGTSFGIAAKYQLDPTTSISAKVNNSS*IGVGCTQTLRPAVKLSLSAVVDGKSINAGSHKLGLALELE

Parental  A
          A
Retrocopy A

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	2.92 RPM	101.01 RPM
SRP014902_testis	12.31 RPM	60.54 RPM
SRP018288_heart	0.71 RPM	296.96 RPM
SRP018288_kidney	0.30 RPM	173.86 RPM
SRP018288_liver	0.00 RPM	66.36 RPM
SRP018288_lung	0.20 RPM	88.28 RPM
SRP018856_adipose	0.61 RPM	115.61 RPM
SRP035408_brain	0.13 RPM	77.75 RPM
SRP035408_liver	0.06 RPM	53.99 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_791 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_791 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_791 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,