RetrogeneDB ID:

retro_sscr_504

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:15:91166401..91166626(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MRPL42
Ensembl ID:ENSSSCG00000030478
Aliases:None
Description:mitochondrial ribosomal protein L42 [Source:HGNC Symbol;Acc:14493]


Retrocopy-Parental alignment summary:






>retro_sscr_504
ATGGCATTGGCAGCAGTAAAATGGGCCATATCAAGCAGAGCTGTCTTGAAACATTTATTTCCAGTTCAAAGTGGAGCCCC
ATATTTCATTTGTTGTAAACCTACATATTCTTCTCTCCCAGATAACTATAATTGCAAAGGAGAGCTTGCTTTGATGTCTG
ATGGCAGGACAATAGTATGTTGTCACCCTTCTGTGGACATTCCACATGAACACACAAAACCTGTG

ORF - retro_sscr_504 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.33 %
Parental protein coverage: 58.59 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMALAAVKWVISSRTILKHLFPIQNSASYCVCHKSTYSSLPDDYNCKVELALTSDGRTIVCYHPSVDIPYE
MALAAVKW.ISSR..LKHLFP.Q..A.Y..C.K.TYSSLPD.YNCK.ELAL.SDGRTIVC.HPSVDIP.E
RetrocopyMALAAVKWAISSRAVLKHLFPVQSGAPYFICCKPTYSSLPDNYNCKGELALMSDGRTIVCCHPSVDIPHE
ParentalHTKPI
HTKP.
RetrocopyHTKPV

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 4 .25 RPM
SRP014902_testis 0 .00 RPM 6 .65 RPM
SRP018288_heart 0 .00 RPM 36 .33 RPM
SRP018288_kidney 0 .00 RPM 16 .06 RPM
SRP018288_liver 0 .00 RPM 13 .59 RPM
SRP018288_lung 0 .00 RPM 7 .13 RPM
SRP018856_adipose 0 .00 RPM 4 .85 RPM
SRP035408_brain 0 .00 RPM 20 .20 RPM
SRP035408_liver 0 .00 RPM 23 .43 RPM
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_504 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_504 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_504 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 19 parental genes, and 74 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000098321 retrocopy
Bos taurus ENSBTAG000000027083 retrocopies
Callithrix jacchus ENSCJAG000000328254 retrocopies
Homo sapiens ENSG000001980153 retrocopies
Gorilla gorilla ENSGGOG000000227605 retrocopies
Loxodonta africana ENSLAFG000000137791 retrocopy
Macaca mulatta ENSMMUG000000168053 retrocopies
Nomascus leucogenys ENSNLEG000000056995 retrocopies
Oryctolagus cuniculus ENSOCUG000000109287 retrocopies
Ochotona princeps ENSOPRG000000109675 retrocopies
Procavia capensis ENSPCAG000000037911 retrocopy
Pongo abelii ENSPPYG000000048337 retrocopies
Pan troglodytes ENSPTRG000000227913 retrocopies
Rattus norvegicus ENSRNOG000000427404 retrocopies
Sus scrofa ENSSSCG00000030478 4 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000002654412 retrocopies
Tarsius syrichta ENSTSYG000000063703 retrocopies
Tursiops truncatus ENSTTRG000000033122 retrocopies
Vicugna pacos ENSVPAG000000076581 retrocopy



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