RetrogeneDB ID:

retro_sscr_364

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:13:20010669..20011047(-)
Located in intron of:ENSSSCG00000011230
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS7
Ensembl ID:ENSSSCG00000027353
Aliases:None
Description:ribosomal protein S7 [Source:HGNC Symbol;Acc:10440]


Retrocopy-Parental alignment summary:






>retro_sscr_364
GTTCCCGTTCCCCAACTGAAGTCTTTCTGGAAAATCCAAGTCTAGCTCGTGCAGGAGTTGGAGAAGTTGTTCCGTGGGAA
GCATGTTGTCTTCATCACTCAGGGGAGAATTCTGCCTAAGCCAACTTGAAAAAGCAGTACAAAAAATAAGCAAAAGCATC
CCAGGAGCTGCACGCCAACAGCTATGCCCAGTGCCGTCCTGGAGGACTTGATTTTCCTGAGGGGGATCGTGGGCAAGAGA
ATCTGTGTGAGGCTGGGCAGCAGCTGCCTCATAAAGGTCCATTTGGACAAAGCACAGCACAACAACGTGGAGCACAAGGT
TGAAACATTTTCTGGTGTCTAGAAGAAGTTCATGGGCAAGGATGTTAATTTTGAATTC

ORF - retro_sscr_364 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.98 %
Parental protein coverage: 64.95 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTAVHDAILEDL
VPVPQLKSF.KIQV.LV.ELEK.F.GKHVVFI.Q.RILPKPT.KS.TKNKQK.PRS.T.TA...A.LEDL
RetrocopyVPVPQLKSFWKIQV*LVQELEKLFRGKHVVFITQGRILPKPT*KSSTKNKQKHPRSCTPTAMPSAVLEDL
ParentalVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTGKDVNFEF
.F...IVGKRI.V.L..S.LIKVHLDKAQ.NNVEHKVETFSGV.KK..GKDVNFEF
RetrocopyIFLRGIVGKRICVRLGSSCLIKVHLDKAQHNNVEHKVETFSGV*KKFMGKDVNFEF

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 595 .70 RPM
SRP014902_testis 0 .00 RPM 1672 .18 RPM
SRP018288_heart 0 .00 RPM 389 .26 RPM
SRP018288_kidney 0 .00 RPM 502 .67 RPM
SRP018288_liver 0 .00 RPM 405 .85 RPM
SRP018288_lung 0 .00 RPM 760 .34 RPM
SRP018856_adipose 0 .15 RPM 801 .54 RPM
SRP035408_brain 0 .00 RPM 613 .80 RPM
SRP035408_liver 0 .00 RPM 805 .64 RPM
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_364 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_364 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_364 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 16 parental genes, and 89 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000184352 retrocopies
Callithrix jacchus ENSCJAG000000164622 retrocopies
Dasypus novemcinctus ENSDNOG0000001328514 retrocopies
Equus caballus ENSECAG000000202532 retrocopies
Felis catus ENSFCAG000000232432 retrocopies
Gorilla gorilla ENSGGOG0000002309513 retrocopies
Loxodonta africana ENSLAFG0000001508711 retrocopies
Myotis lucifugus ENSMLUG000000061211 retrocopy
Macaca mulatta ENSMMUG000000118707 retrocopies
Nomascus leucogenys ENSNLEG0000001540710 retrocopies
Otolemur garnettii ENSOGAG000000281651 retrocopy
Pan troglodytes ENSPTRG000000116153 retrocopies
Pteropus vampyrus ENSPVAG000000020717 retrocopies
Sus scrofa ENSSSCG00000027353 5 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000248303 retrocopies
Tursiops truncatus ENSTTRG000000016166 retrocopies



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