RetrogeneDB ID: retro_sscr_178

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:138180496..138181462(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEH1L
• Ensembl ID: ENSSSCG00000030252
• Aliases: None
• Description: SEH1-like (S. cerevisiae) [Source:HGNC Symbol;Acc:30379]

Sequence

>retro_sscr_178
GTCTGGGACAAAACTGAAAGTGGGGATTGCCATTGCATTGCTAGCTGGAAGACACATAGTGGATCGGTGTGGTGTGTGAC
GTGGGCCCATCCTGAATTTGGCCAGGTTTTGGCTTCCTGTTCTTTTGACCGAACAGCTGCTGTATGGGAAGAAATAATAG
GAGAATCAAATGATAAACTGTGAGGATACAGCCACTGGGTAAAGAGGACATGGCTAGTGGACAGTAGGACATCTGTTACC
CATGTGAAGTTTGCATCCAAGCATATGGGTCTTATGTTAGCCACTTGCCCTGCAGACAGTATAGTAAGAATATATGAGGT
GCCAAATGTCATGAACCTCAACTAGTGGTCTCTGCAGCATGAGGTTTCCTGCAAGCTAAGCTGCAGTTGCATTTCTTGGA
ATCCTTCAAGCTCTCGCTCACCCCTGCCATGATCGCAGTGGGCAGCAACAACAGTAGTCCTAATGCAATGGCCAAGGTGC
ACATTTTCGAATATAATGAGAACGCCAGGAAATATGCCAAAGCCAAAACCCTCATGACAGTCACAGATCCTGTCCATGAC
ATTGCTTTTGCTCCAAACTTGGGGAGGTCTTTCTACATCCTAGGCATAGCAATCAAAGATGTGAGAATTTTTACACTAAA
GCCTGTGAGAAAAGAACTTATTTCTCCCAGTGGGCCAACCAAATTTGAAATCCAGGAGGTGGTTCAGTTTGATAATCATA
ATTCCCAGGTCTGGCAAGTGAGCTGGAATATAATAGGGACAGTGCTGTCGTCTCAGGAGACATGGCTGTGTACAACTGTG
GAAAGCTAACTATATGGACAACTGGAAGTGCACTGGGATTCTGAAAGGTAATGGGAACCCTGTCAGTGGGAGTTCTCAGC
AGGGAAATACAAATCCTTCCCTAGGTTCAAATATCCCAAATCTGCAGCATTCACTAAATGAATCTTCTGCTGACAGAAAG
CACAGC

Alignment

ORF - retro_sscr_178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.63 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VWDKSESGDWHCTASWKTHSGSVWRVTWAHPEFGQVLASCSFDRTAAVWEEIVGESNDKLRGQSHWVKRT
          VWDK.ESGD.HC.ASWKTHSGSVW.VTWAHPEFGQVLASCSFDRTAAVWEEI.GESNDKL.G.SHWVKRT
Retrocopy VWDKTESGDCHCIASWKTHSGSVWCVTWAHPEFGQVLASCSFDRTAAVWEEIIGESNDKL*GYSHWVKRT

Parental  TLVDSRTSVTDVKFAPKHMGLMLATCSADGIVRIYEAPDVMNLSQWSLQHEVSCKLSCSCISWNPSSSRA
          .LVDSRTSVT.VKFA.KHMGLMLATC.AD.IVRIYE.P.VMNL..WSLQHEVSCKLSCSCISWNPSSSR.
Retrocopy WLVDSRTSVTHVKFASKHMGLMLATCPADSIVRIYEVPNVMNLN*WSLQHEVSCKLSCSCISWNPSSSRS

Parental  -HPPMIAVGSDDGSPNAMAKVQIFEYNENTRKYAKAETLMTVTDPVHDIAFAPNLGRSFHILAIATKDVR
          ..P.MIAVGS...SPNAMAKV.IFEYNEN.RKYAKA.TLMTVTDPVHDIAFAPNLGRSF.IL.IA.KDVR
Retrocopy <TPAMIAVGSNNSSPNAMAKVHIFEYNENARKYAKAKTLMTVTDPVHDIAFAPNLGRSFYILGIAIKDVR

Parental  IFTLKPVSRKELTSSGGPTKFEIQVVAQFDNHNSQVWRVSWNITGTVLAS-SGD-DGCVRLWKANYMDNW
          IFTLKPV.RKEL.S..GPTKFEIQ.V.QFDNHNSQVW.VSWNI.GTVL.S.SGD..GCV.LWKANYMDNW
Retrocopy IFTLKPV-RKELISPSGPTKFEIQEVVQFDNHNSQVWQVSWNIIGTVLSS<SGD<HGCVQLWKANYMDNW

Parental  KCTGILKGNGSPVSGSSQQGNANPSLGSNTPNLQHSLNGSSASRKHS
          KCTGILKGNG.PVSGSSQQGN.NPSLGSN.PNLQHSLN.SSA.RKHS
Retrocopy KCTGILKGNGNPVSGSSQQGNTNPSLGSNIPNLQHSLNESSADRKHS

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	4.91 RPM
SRP014902_testis	0.00 RPM	8.06 RPM
SRP018288_heart	0.00 RPM	9.98 RPM
SRP018288_kidney	0.00 RPM	8.96 RPM
SRP018288_liver	0.00 RPM	8.32 RPM
SRP018288_lung	0.00 RPM	12.73 RPM
SRP018856_adipose	0.00 RPM	17.10 RPM
SRP035408_brain	0.00 RPM	3.94 RPM
SRP035408_liver	0.00 RPM	5.37 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_178 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_178 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_178 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000545	2 retrocopies	retro_chof_165, retro_chof_2594,
Oryctolagus cuniculus	ENSOCUG00000006858	2 retrocopies	retro_ocun_1723, retro_ocun_1801,
Sus scrofa	ENSSSCG00000030252	2 retrocopies	retro_sscr_178 , retro_sscr_186,