RetrogeneDB ID: retro_sscr_267

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 11:53265330..53265932(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC7
• Ensembl ID: ENSSSCG00000002667
• Aliases: None
• Description: zinc finger, DHHC-type containing 7 [Source:HGNC Symbol;Acc:18459]

Sequence

>retro_sscr_267
GCAGTCCCCAAAGGCGGTGATAATAAAGAATAGGTAGAAGAGTTTGCAGCTGAAGCCGGAAGAAGTGATCTACAAGCACC
CACAGTGCCGCTGTATCAAGCGCAGCATGCCCACTGCACTGCAGGACTTGCAAAAGAGGTATTGGGAAATATATCAGCAC
TGCCCTGGGTGCACAATTGCGTAGGAGGAAAGAAGCAGAGGGTTTTTTGTGCCCTTCACTTGGTACAAAGCTCTGTCATC
AGCGCCACGCTAGTCCTTTGCGGGCTCCAGTTCATCTGGAAACGTGGGCAGTGGTTTGAATGCAGTGATATTTCGCCTCC
TGTAACTATAATCCTGCTAATCTTTCTGTGCCTTGAGGGTCTCTGTCTTTTCACTTTCACTGCAGGGATGTTCTGAATCC
ACTTCAGTTCAATATGCAATGACAAAACGGAGATCCAGTGGCTGAAGAGTAAGAAGCCCATGTGTGAGTGGAGTCTGCCA
TGGGAAGGGATAAAGTTGGTCTCTGGGGGCTCCCCTCGATGCTCTGAATGAACCCCTTCGTCAGCTTGCAGTTTAAGCGA
CTTCAAATGAGACCCTGGAAAGGCGACCCAGAGTTCTCTGTG

Alignment

ORF - retro_sscr_267 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.87 %
• Parental protein coverage: 65.58 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  AVPKGNATKEFME-SLQLKPGEVIYKCPKCCCIKPERAHHCSICKRCIRKMDHHC-PWVNNCVGEKNQR-
          AVPKG...KE..E.SLQLKP.EVIYK.P.C.CIK...................HC.PWV.NCVG.K.QR.
Retrocopy AVPKGGDNKE*VE>SLQLKPEEVIYKHPQCRCIKRSMPTALQDLQKRYWEIYQHC<PWVHNCVGGKKQR>

Parental  FFVLFTMYIALASV-HALVLCGLQFISCVRGQWTECSGFSPPVTVILLIFLCLEGLLFFTFTAVMFGTQI
          FFV.FT.Y.AL.S....LVLCGLQFI...RGQW.ECS..SPPVT.ILLIFLCLEGL..FTFTA.MF....
Retrocopy FFVPFTWYKALSSA<ATLVLCGLQFI-WKRGQWFECSDISPPVTIILLIFLCLEGLCLFTFTAGMF*IHF

Parental  HSICNDETEIERLKSEKPTWERRLRWEGMKSVFGGP-PSLLWMNPFVGFRLRRLQTRPRKGGPEFSV
          .SICND.TEI..LKS.KP..E..L.WEG.K.V.GG..PS.L.MNPFV.....RLQ.RP.KG.PEFSV
Retrocopy SSICNDKTEIQWLKSKKPMCEWSLPWEGIKLVSGGS<PSML*MNPFVSLQFKRLQMRPWKGDPEFSV

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	74.06 RPM
SRP014902_testis	0.14 RPM	67.19 RPM
SRP018288_heart	0.03 RPM	18.13 RPM
SRP018288_kidney	0.00 RPM	98.11 RPM
SRP018288_liver	0.00 RPM	22.23 RPM
SRP018288_lung	0.00 RPM	83.50 RPM
SRP018856_adipose	0.18 RPM	56.58 RPM
SRP035408_brain	0.00 RPM	24.07 RPM
SRP035408_liver	0.00 RPM	22.63 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_267 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_267 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_267 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004119	1 retrocopy	retro_cjac_1437,
Echinops telfairi	ENSETEG00000016077	1 retrocopy	retro_etel_1105,
Microcebus murinus	ENSMICG00000011194	1 retrocopy	retro_mmur_1362,
Macaca mulatta	ENSMMUG00000020674	1 retrocopy	retro_mmul_1448,
Sus scrofa	ENSSSCG00000002667	1 retrocopy	retro_sscr_267 ,
Sus scrofa	ENSSSCG00000005658	1 retrocopy	retro_sscr_250,
Tursiops truncatus	ENSTTRG00000016028	1 retrocopy	retro_ttru_363,