RetrogeneDB ID:

retro_sscr_670

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:2:63197076..63197616(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PLA2G12A
Ensembl ID:ENSSSCG00000009139
Aliases:None
Description:phospholipase A2, group XIIA [Source:HGNC Symbol;Acc:18554]


Retrocopy-Parental alignment summary:






>retro_sscr_670
CCCCCACAGCCCATGCTGGCCATCATCCTCAACCACAGCTTTTGGTTGCTGGGAGCAAGCCCAGACCATCGACTGGAGGG
CCACCCTGCAGACTAACCAGAGCAGCAGTCAGAATATAGACACATACCTGAACTCCATTTTAGACGTCTTGGCAGGTCAG
GATTGGCTCTGCTAGTATCAATGCAGTGATGGATCTAAGCCTTTCCCACGTTAGGATTATATACCCTCCCTGCCTAAGGG
ATGTGGTTTTTTACTCTTTGATGTTCATTGGAATATTGGCATCCCATCCCTGACAAAGTGCTGCAACCAAGCAACGGGTG
CTATGAGACCTGTGGCAAAAGCAACAAGGACTGGAATGAGGAGTTCCAGTATTGTCCCTCCAAGATTTGCTGAGATGTGC
AGAAAACACTAGAACCAACTCAATGTATTCAGGCACTTGAAACCACAGTGGAGCTCTTGTCTGACAGTGTTATGCATTTA
GCCTGTAAATCATACCTGGACAGTCAACGAGCTGCCTGTAGGTGTTGCTGGGAAGAAAAA

ORF - retro_sscr_670 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.48 %
Parental protein coverage: 95.24 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalPALALLLLLL-TAAFRCQEQAQPTDWRATLKTIRNGVHKIDTYLNAALDLLGGEDGLCQYKCNDGSKPFP
P....L...L.T.AF.C.EQAQ..DWRATL.T.......IDTYLN..LD.L.G.D.LC.Y.C.DGSKPFP
RetrocopyPPQPMLAIIL>TTAFGCWEQAQTIDWRATLQTNQSSSQNIDTYLNSILDVLAGQDWLC*YQCSDGSKPFP
ParentalRYGYKPSPPNGCGSPLFGVHLNIGIPSLTKCCNQ-HDRCYETCGKSKNDCDEEFQYCLSKICRDVQKTLG
R..Y.PS.P.GCG..LF.VH.NIGIPSLTKCCNQ....CYETCGKS..D..EEFQYC.SKIC.DVQKTL.
RetrocopyR*DYIPSLPKGCGFLLFDVHWNIGIPSLTKCCNQ<SNGCYETCGKSNKDWNEEFQYCPSKIC*DVQKTLE
ParentalLAQHIQACETTVELLFDSVIHLGCKPYLDSQRAACRCRYQEK
..Q.IQA.ETTVELL.DSV.HL.CK.YLDSQRAACRC...EK
RetrocopyPTQCIQALETTVELLSDSVMHLACKSYLDSQRAACRCCWEEK

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 44 .73 RPM
SRP014902_testis 0 .00 RPM 38 .33 RPM
SRP018288_heart 0 .00 RPM 36 .57 RPM
SRP018288_kidney 0 .00 RPM 25 .32 RPM
SRP018288_liver 0 .00 RPM 28 .30 RPM
SRP018288_lung 0 .00 RPM 25 .66 RPM
SRP018856_adipose 0 .00 RPM 20 .77 RPM
SRP035408_brain 0 .00 RPM 25 .92 RPM
SRP035408_liver 0 .00 RPM 27 .24 RPM
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_670 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_670 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_670 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 14 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000152301 retrocopy
Callithrix jacchus ENSCJAG000000161692 retrocopies
Dasypus novemcinctus ENSDNOG000000165737 retrocopies
Homo sapiens ENSG000001237391 retrocopy
Gorilla gorilla ENSGGOG000000010822 retrocopies
Loxodonta africana ENSLAFG000000008522 retrocopies
Mustela putorius furoENSMPUG000000086371 retrocopy
Mus musculus ENSMUSG000000279991 retrocopy
Otolemur garnettii ENSOGAG000000046861 retrocopy
Ochotona princeps ENSOPRG000000145052 retrocopies
Pan troglodytes ENSPTRG000000163621 retrocopy
Sus scrofa ENSSSCG00000009139 3 retrocopies
retro_sscr_622, retro_sscr_623, retro_sscr_670 ,
Tarsius syrichta ENSTSYG000000047564 retrocopies
Vicugna pacos ENSVPAG000000098421 retrocopy



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