RetrogeneDB ID:

retro_sscr_1208

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:X:85310412..85310921(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSSCG00000031055
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SRM
Ensembl ID:ENSSSCG00000027689
Aliases:None
Description:spermidine synthase [Source:HGNC Symbol;Acc:11296]


Retrocopy-Parental alignment summary:






>retro_sscr_1208
AGGATGTCATTCAAGTCTCTGCCGGGCATGGCCGTTGGCTATTTGAACTCAAAGATGACCCTACTTGTGGGTGATGGTTT
TGCGTTCATGAAACAGAACTGGGATGTTTTCGATGGCATTGTCACTGACTCCTCAGACCCCCTGGGCCCTGCTGAGAGTA
TCTTCAAGGAATCCTATTATCGGCTCATGAAGACAGCACTTAAGAAGGATGGCACCCTCTGCTGCTAGGGCTAGTGTCAG
TGGCTGCACCTGAACCTCATCAAGGAGATGGGACAGTTCTGCGAATCATTGTTCCTGGCGGTGGGCTATGCTTACTGCAC
CATCACCCCCTACCCCAGTGGCCAAATTGGCTTCATGCTGTGCAGCAAAATCCAAGCACCAACTTCCCCAAGCCTGTGCA
GCAGCTGACACAGAAGCATGTGGTACAGATGCCACTGAAATTCTACAAAAATGACTTGCACCAGGCAGCCTTTGTCCTGC
CCTATTTTGCCTACAAGGCCCTGAATGAT

ORF - retro_sscr_1208 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.1 %
Parental protein coverage: 56.29 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalQVSKKFLPGMAVSYSSSKLTLHVGDGFEFMKQNQDAFDVIITDSSDPMGPAESLFKESYYQLMKTALKEE
..S.K.LPGMAV.Y..SK.TL.VGDGF.FMKQN.D.FD.I.TDSSDP.GPAES.FKESYY.LMKTALK..
RetrocopyRMSFKSLPGMAVGYLNSKMTLLVGDGFAFMKQNWDVFDGIVTDSSDPLGPAESIFKESYYRLMKTALKKD
ParentalGILCCQGECQWLHLDLIKEMRQFCKSLFPVVDYAYCTIPTYPSGQIGFMLCSK-NPSTNFREPVQLLTQK
G.LCC.G.CQWLHL.LIKEM.QFC.SLF..V.YAYCTI..YPSGQIGFMLCSK.NPSTNF..PVQ.LTQK
RetrocopyGTLCC*G*CQWLHLNLIKEMGQFCESLFLAVGYAYCTITPYPSGQIGFMLCSK<NPSTNFPKPVQQLTQK
ParentalQVEQRQLRYYNSDVHRAAFVLPEFARKALND
.V.Q..L..Y..D.H.AAFVLP.FA.KALND
RetrocopyHVVQMPLKFYKNDLHQAAFVLPYFAYKALND

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 19 .64 RPM
SRP014902_testis 0 .00 RPM 40 .74 RPM
SRP018288_heart 0 .00 RPM 8 .83 RPM
SRP018288_kidney 0 .00 RPM 16 .84 RPM
SRP018288_liver 0 .00 RPM 32 .14 RPM
SRP018288_lung 0 .00 RPM 13 .64 RPM
SRP018856_adipose 0 .00 RPM 26 .15 RPM
SRP035408_brain 0 .00 RPM 57 .11 RPM
SRP035408_liver 0 .00 RPM 39 .75 RPM
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_1208 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_1208 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_1208 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species Parental gene accession Retrocopies number
Gorilla gorilla ENSGGOG000000143851 retrocopy
Macropus eugenii ENSMEUG000000070022 retrocopies
Myotis lucifugus ENSMLUG000000175851 retrocopy
Macaca mulatta ENSMMUG000000193212 retrocopies
Mustela putorius furoENSMPUG000000164351 retrocopy
Sus scrofa ENSSSCG00000027689 1 retrocopy
retro_sscr_1208 ,



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