RetrogeneDB ID:

retro_sscr_1088

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:GL893298.2:34010..34294(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HSPE1
Ensembl ID:ENSSSCG00000016078
Aliases:None
Description:heat shock 10kDa protein 1 (chaperonin 10) [Source:HGNC Symbol;Acc:5269]


Retrocopy-Parental alignment summary:






>retro_sscr_1088
AGAAAGTTTCTTTCTCTCTTTGACCGGGTCTTAGTTGAAAGAAGTGCAGCTGAAACTGTAATCAAAGGATGCATTCTGTA
CCCAGAAAAATCTCAAGGAAAAGTACTGCAAGGAACAGCAGTAGCTGTTGGATCAGGCTCTGAAGGAAAGGGTGGAGAGA
GTCAACAAGTTGTGTGAAACTTGGAAATAAAGTTCTTCTGTCAGAACATGGAGGCTCCAAAGCAGTTCTGGACGACAAGG
ATTATTTCTTACTTAGAGCTGGTGATGTCCTCGGAAAGTATGTA

ORF - retro_sscr_1088 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.08 %
Parental protein coverage: 93.14 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalRKFLPLFDRVLVERSAAETVTKGGIMLPEKSQGKVLQATVVAVGSGSKGKGGEIQPV-SVKVGDKVLLPE
RKFL.LFDRVLVERSAAETV.KG.I..PEKSQGKVLQ.T.VAVGSGS.GKGGE.Q.V..VK.G.KVLL.E
RetrocopyRKFLSLFDRVLVERSAAETVIKGCILYPEKSQGKVLQGTAVAVGSGSEGKGGESQQV<CVKLGNKVLLSE
ParentalYGGTRVVLDDKDYFLFRDGDILGKYV
.GG...VLDDKDYFL.R.GD.LGKYV
RetrocopyHGGSKAVLDDKDYFLLRAGDVLGKYV

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP014902_placenta 0 .00 RPM 15 .13 RPM
SRP014902_testis 0 .00 RPM 131 .26 RPM
SRP018288_heart 0 .00 RPM 147 .37 RPM
SRP018288_kidney 0 .00 RPM 329 .99 RPM
SRP018288_liver 0 .00 RPM 397 .54 RPM
SRP018288_lung 0 .00 RPM 18 .94 RPM
SRP018856_adipose 0 .00 RPM 93 .50 RPM
SRP035408_brain 0 .00 RPM 75 .65 RPM
SRP035408_liver 0 .00 RPM 187 .41 RPM
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_1088 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_1088 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_1088 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 9 parental genes, and 90 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000040081 retrocopy
Dasypus novemcinctus ENSDNOG0000001324627 retrocopies
Homo sapiens ENSG0000011554118 retrocopies
Gorilla gorilla ENSGGOG0000002794417 retrocopies
Macaca mulatta ENSMMUG000000104911 retrocopy
Procavia capensis ENSPCAG000000095411 retrocopy
Pongo abelii ENSPPYG000000258761 retrocopy
Pan troglodytes ENSPTRG0000001277417 retrocopies
Sus scrofa ENSSSCG00000016078 7 retrocopies



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