RetrogeneDB ID: retro_sscr_203

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:279893219..279893834(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DEK
• Ensembl ID: ENSSSCG00000001075
• Aliases: None
• Description: DEK oncogene [Source:HGNC Symbol;Acc:2768]

Sequence

>retro_sscr_203
TTAATCATGGAAAGCAAGAGGGAAAAGAAAAAAAGTAGGCTGACAATGCAAGTCTCTTCCTTACAAAGAGAGCCATTTAC
AATTGCACAAGGAAAGCGGCAGAAATTTTGTGAAATTGAAAGGATACATTTTTTTTTTCTAAGTAAGAAGAAAACAGATG
AGCTTAGAAATCTACATAAGCTCTTTATAACAGACCAGGCACAGTGTCCTCTTTAAAGAAGAATGTGTGTCAAGTTCAGT
GGCTTTCCATTTGGAAAAAGAAGTATCCAATATAAAAAGAAGGAAGAAATGTTAAAAAAAAAAAAATTAGAAATGCCATG
TTAACGAGCATCTGTGAGGTTCTTGGAAAGATCAGGTGTAAATAGTGAACTGGTGAAAAGGATCTTGAATTTCTTAATGC
ATCCAAAGCCTTCTGGCAAACCATTTCCAAAGTCTGAAAAAACCTCTAGCAAAAGCCACAAAAAAGAACGGAATAATTCT
GGAATGGCCAGGAAAGCTAAGCAAACCAAATGTCCTGAAATTCTGTCGGATGAATTCAGCAGTGATAAAGCTGAGAAGAA
AAATAAGGGAGAGTCTTCTGATGAGGAAGATAAAGAAATTGAAGAGGAGCCACCT

Alignment

ORF - retro_sscr_203 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.29 %
• Parental protein coverage: 55.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LIVEGKREKKKVERLTMQVSSLQREPFTIAQGKGQKLCEIERIHFF-LSKKKTDELRNLHKL-LYNRPGT
          LI.E.KREKKK..RLTMQVSSLQREPFTIAQGK.QK.CEIERI....LSKKKTDELRNLHKL.LYNRPGT
Retrocopy LIMESKREKKK-SRLTMQVSSLQREPFTIAQGKRQKFCEIERIXXXXLSKKKTDELRNLHKL<LYNRPGT

Parental  VSSLKKNVGQ-FSGFPFEKGSIQYKKKEEMLKKFRNAMLKSICEVLDLERSGVNSELVKRILNFLMHPKP
          VSSLKKNV.Q.FSGFPF.K.SIQYKKKEEM.......M......V..LERSGVNSELVKRILNFLMHPKP
Retrocopy VSSLKKNVCQ>FSGFPFGKRSIQYKKKEEMXXXXXLEMPC*RASVRFLERSGVNSELVKRILNFLMHPKP

Parental  SGKPLPKSKKTSSKGNKKERNSSGMARKAKRTKCPEILSDESSSDEDEKKNKEESSDEEDKESEEEPP
          SGKP.PKS.KTSSK..KKERN.SGMARKAK.TKCPEILSDE.SSD..EKKNK.ESSDEEDKE.EEEPP
Retrocopy SGKPFPKSEKTSSKSHKKERNNSGMARKAKQTKCPEILSDEFSSDKAEKKNKGESSDEEDKEIEEEPP

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	7.17 RPM
SRP014902_testis	0.00 RPM	27.44 RPM
SRP018288_heart	0.00 RPM	66.56 RPM
SRP018288_kidney	0.00 RPM	82.35 RPM
SRP018288_liver	0.00 RPM	39.18 RPM
SRP018288_lung	0.00 RPM	124.53 RPM
SRP018856_adipose	0.00 RPM	33.17 RPM
SRP035408_brain	0.00 RPM	78.26 RPM
SRP035408_liver	0.00 RPM	122.59 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_203 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_203 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_203 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010184	1 retrocopy	retro_cfam_1362,
Echinops telfairi	ENSETEG00000018188	1 retrocopy	retro_etel_1367,
Loxodonta africana	ENSLAFG00000004470	1 retrocopy	retro_lafr_517,
Macaca mulatta	ENSMMUG00000019763	2 retrocopies	retro_mmul_1266, retro_mmul_2627,
Otolemur garnettii	ENSOGAG00000007750	1 retrocopy	retro_ogar_3258,
Sus scrofa	ENSSSCG00000001075	1 retrocopy	retro_sscr_203 ,