RetrogeneDB ID:

retro_sscr_1089

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:GL893305.1:60320..60569(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SUMO3
Ensembl ID:ENSSSCG00000024026
Aliases:None
Description:small ubiquitin-like modifier 3 [Source:HGNC Symbol;Acc:11124]


Retrocopy-Parental alignment summary:






>retro_sscr_1089
AAAGAAAAGCCCAAGGAAGGAGTTAAGGCTGAGAACAATAATCAAACTAATCTGAAGATGGCAGGGATGGTTCTGTGGTG
CAGTTTAAGATTAAGAGACAAACAACACTTAGTAAACTAATGAAAGCCTACTGTGAATGACAAGAGTTTGTCAAGGAGGA
AAATCTGATTCCAAACTGATAGTCAGCCAATCAATGAAACAGACACACCAGCAGAGTTGGAAATAAAAGATGAAGATGCA
ATCGATGTA

ORF - retro_sscr_1089 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.24 %
Parental protein coverage: 79.81 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalEEKPKEGVKTENDH-INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQ-GLSMRQIRFRFDGQPINEAD
.EKPKEGVK.EN....N....G.DGSVVQFKIKR.T.LSKLMKAYCE.Q..LS.R.I.F..D.QPINE.D
RetrocopyKEKPKEGVKAENNN<SN*SEDGRDGSVVQFKIKRQTTLSKLMKAYCE*Q>SLSRRKI*FQTDSQPINETD
ParentalTPAQLEMEDEDTIDV
TPA.LE..DED.IDV
RetrocopyTPAELEIKDEDAIDV

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 122 .64 RPM
SRP014902_testis 0 .00 RPM 86 .00 RPM
SRP018288_heart 0 .00 RPM 19 .44 RPM
SRP018288_kidney 0 .00 RPM 72 .20 RPM
SRP018288_liver 0 .00 RPM 66 .20 RPM
SRP018288_lung 0 .00 RPM 47 .45 RPM
SRP018856_adipose 0 .00 RPM 54 .81 RPM
SRP035408_brain 0 .00 RPM 121 .80 RPM
SRP035408_liver 0 .00 RPM 68 .99 RPM
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_1089 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_1089 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_1089 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Bos taurus retro_btau_260

Parental genes homology:
Parental genes homology involve 18 parental genes, and 94 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000020713 retrocopies
Bos taurus ENSBTAG000000173213 retrocopies
Bos taurus ENSBTAG000000301698 retrocopies
Callithrix jacchus ENSCJAG0000001052920 retrocopies
Felis catus ENSFCAG000000265504 retrocopies
Microcebus murinus ENSMICG000000110112 retrocopies
Myotis lucifugus ENSMLUG000000253424 retrocopies
Myotis lucifugus ENSMLUG000000286012 retrocopies
Macaca mulatta ENSMMUG000000067603 retrocopies
Mustela putorius furoENSMPUG000000102341 retrocopy
Mustela putorius furoENSMPUG000000139549 retrocopies
Oryctolagus cuniculus ENSOCUG000000217394 retrocopies
Rattus norvegicus ENSRNOG000000384891 retrocopy
Sus scrofa ENSSSCG0000001721215 retrocopies
Sus scrofa ENSSSCG00000024026 2 retrocopies
retro_sscr_1089 , retro_sscr_320,
Ictidomys tridecemlineatus ENSSTOG000000105872 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000002468510 retrocopies
Takifugu rubripes ENSTRUG000000148921 retrocopy



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