RetrogeneDB ID: retro_sscr_1195

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:61234382..61234813(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CERS5
• Ensembl ID: ENSSSCG00000024932
• Aliases: None
• Description: ceramide synthase 5 [Source:HGNC Symbol;Acc:23749]

Sequence

>retro_sscr_1195
ATGTGGAGATTCACCTTCTATTTATATATATTCTGCTACAGAATTAGCCTTCTCTGGTCCTCTCCTTAGTTTTGGAACAC
CGGATGATGCTGGCACAGTTACCCTTACCAGCCTCTCACAAGTGGGCTTTATTACTATTATATCATGGAATTGGCTTTCT
TTTGGTCTCATGTTTTCTCAGTTACAGACATTTAAAGAAAGGACTTTCTGATCATGTTCGTGCATCATATGGCCACCATT
GGGTTCATTACCTTCTTCTACATCAACAACATGATTCGAGTGGGAATTCTGGTCATGCATCTATATGACTTCTTGCTGGA
GGCAGCCAAGCTGACCAATTATGCCAAGTATCATAATGACTTGTGACACCATTTTTTGTGATCTTCAGTGCTATTTTTGT
GGTGATGCATCTAGGAATCTATGCATTCTGG

Alignment

ORF - retro_sscr_1195 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.17 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MWRFTFYLCIFCYGIRFLWSSPWFWDTRQCWHSYPYQPLTSGLYYYYIMELAFYWSLMFSQFTDIKRKDF
          MWRFTFYL.IFCY.I..LWSSP.FW.T..CWHSYPYQPLTSGLYYYYIMELAF.WS..FS..TDI.RKDF
Retrocopy MWRFTFYLYIFCYRISLLWSSP*FWNTG*CWHSYPYQPLTSGLYYYYIMELAFFWSHVFS-VTDI*RKDF

Parental  LIMFVHHLATIALITFSYINNMVRVGTLVMCLHDASDFLLEAAKLANYAKYQR-LCDTL-FVVFSAVFVV
          LIMFVHH.ATI..ITF.YINNM.RVG.LVM.L.D...FLLEAAKL.NYAKY....CDT..FV.FSA.FVV
Retrocopy LIMFVHHMATIGFITFFYINNMIRVGILVMHLYD---FLLEAAKLTNYAKYHN>TCDTI>FVIFSAIFVV

Parental  TRLGIYPFW
          ..LGIY.FW
Retrocopy MHLGIYAFW

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	9.82 RPM
SRP014902_testis	0.00 RPM	17.68 RPM
SRP018288_heart	0.00 RPM	4.27 RPM
SRP018288_kidney	0.00 RPM	5.71 RPM
SRP018288_liver	0.00 RPM	10.55 RPM
SRP018288_lung	0.00 RPM	6.62 RPM
SRP018856_adipose	0.00 RPM	9.79 RPM
SRP035408_brain	0.00 RPM	1.94 RPM
SRP035408_liver	0.00 RPM	3.82 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1195 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1195 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1195 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000012843	1 retrocopy	retro_ocun_1643,
Otolemur garnettii	ENSOGAG00000004668	1 retrocopy	retro_ogar_392,
Pteropus vampyrus	ENSPVAG00000006713	1 retrocopy	retro_pvam_591,
Sus scrofa	ENSSSCG00000024932	1 retrocopy	retro_sscr_1195 ,