RetrogeneDB ID: retro_sscr_695

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 3:40825695..40826359(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000024561
• Aliases: None
• Description: None

Sequence

>retro_sscr_695
TTTAATGGATTTTTAAAAGACCTCAATGAGGTGAGGATAGGCGTCCTTAAACACTTGCATGGTTTTCTGAAGCTTCTTCC
TATTGACAAAAGAAGACAATATCAGTATCAGGAGTTTGGGGTGACATATAGCCGTCAAAATTGGTGGTTTTGAGCTGAGC
TGGCTGAACGGCTGGTTTACTCCTAGAACTGTACAGCCCCAGAGGTGTCTATGGCTGCTTGTGCTCCACTGTCCTGAGCC
TGTGTGCACATAAAGCATCTTGCATCAGCTGGATTTCCTGCAAGCTGGTCAGCGAGATGGTGCACAAGCATCACCACGCC
ACACCGCCCCCCCTCAGAGTGGGCCTCGTCGTGAGCTGGTGGACATCTTTAGCCGCTGCCCATGCTGGTCAGGGCGCCAG
GCGCTGGTCTTCATCTGCCAGGCTGTCACTGAAGATGACTGCCTTGCCAGAGACCAGTGTGCTCTGCCTCTGATGCCACA
CCCGCTTACCTTGGCCGATGGCAGGATGCCAAATGGATGCGTGCTGCTTGCAAAAACCTTAAGACAGACTCTACTAGAAA
AAGAGTATTTTCTCACCTCTATTCCACAGGAGGCTGTGGAATAGACCATCGCAGCTCTTCAGATGGCTCATGACAGAGAT
GTTAAGTATTTGCTGAGTCTCCAT

Alignment

ORF - retro_sscr_695 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 69.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FNGFLKDLDEVRIGVLKHLHDFLKLLHIDKRREYLYQLQEFLVTDNSRNWRFRAELAEQLI-LLLELYSP
          FNGFLKDL.EVRIGVLKHLH.FLKLL.IDKRR.Y.YQ..EF.VT....NW.F.AELAE.L..LLLELYSP
Retrocopy FNGFLKDLNEVRIGVLKHLHGFLKLLPIDKRRQYQYQ--EFGVTYSRQNWWF*AELAERLV<LLLELYSP

Parental  RDVYDYLRPIALNLCADKVSSVRWISYKLVSEMVRKLHQAAPPSFGVDLI-RELVESFGRCX----RQAF
          R.VY..L....L.LCA.K.S...WIS.KLVSEMV.K.H.A.PP...V.L..RELV..F.RC.....RQA.
Retrocopy RGVYGCLCSTVLSLCAHKASCISWISCKLVSEMVHKHHHATPPPLRVGLV<RELVDIFSRCPCWSGRQAL

Parental  VFVCQTVIEDDCLPMDQFALHLMPHLLTLANDRVPNVRVLLAKTLRQTLLEKECFLTSASCHQEAVEQTI
          VF.CQ.V.EDDCL..DQ.AL.LMPH.LTLA..R.PN..VLLAKTLRQTLLEKE.FLTS....QEAVE.TI
Retrocopy VFICQAVTEDDCLARDQCALPLMPHPLTLADGRMPNGCVLLAKTLRQTLLEKEYFLTSIP--QEAVE*TI

Parental  MALQMDRDSDVKYFASIH
          .ALQM..D.DVKY..S.H
Retrocopy AALQMAHDRDVKYLLSLH

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	57.74 RPM
SRP014902_testis	0.00 RPM	38.90 RPM
SRP018288_heart	0.00 RPM	2.70 RPM
SRP018288_kidney	0.00 RPM	6.40 RPM
SRP018288_liver	0.16 RPM	2.08 RPM
SRP018288_lung	0.00 RPM	14.05 RPM
SRP018856_adipose	0.00 RPM	6.49 RPM
SRP035408_brain	0.03 RPM	1.91 RPM
SRP035408_liver	0.00 RPM	1.14 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_695 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_695 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_695 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000061950	1 retrocopy	retro_mmus_3230,
Sus scrofa	ENSSSCG00000003679	1 retrocopy	retro_sscr_694,
Sus scrofa	ENSSSCG00000024561	1 retrocopy	retro_sscr_695 ,