RetrogeneDB ID:

retro_sscr_160

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:1:82463919..82464251(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSSSCG00000025782
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_sscr_160
GGTCCGGGGGCTGTTTTCCGCAGTTTGGGTGCCTTGTCCGCAGCTGGGGCCTTAGGATTGGCCTCCTACGGAGTGCACAG
AGCCCAGTTTCTGGATGCCTACGGGAAAAGCTCTTTGACAAGGCCAACAAACACCACTTTTTACACAGCCTGGCCCTGTT
AGGGGTGCCCCTGTGCAGAAAACCCCTCTGGGCTGGGTTACTGCTAGCTTCTGGAACCACCTTATTCTGCACCAGCTTTT
ACTACCAGTCTCTTAGCGGAGACCACAGCATCCGGACTTTGGCCCCTGTAAGAGGGAGCCTGCCAATTTGGGGCTGGCTT
GCCTTGGCTCTT

ORF - retro_sscr_160 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.5 %
Parental protein coverage: 98.23 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalGPGAVFRRLGALSGAGALGLASYGAHGAQFPDAYGK-ELFDKTNKHHFLHSLALLGVPLCRKPLWAGLLL
GPGAVFR.LGALS.AGALGLASYG.H.AQF.DAYGK..LFDK.NKHHFLHSLALLGVPLCRKPLWAGLLL
RetrocopyGPGAVFRSLGALSAAGALGLASYGVHRAQFLDAYGK<KLFDKANKHHFLHSLALLGVPLCRKPLWAGLLL
ParentalASGTTLFCTSFYYQALSGDPSIQTLAPVGGSLLILGWLALAL
ASGTTLFCTSFYYQ.LSGD.SI.TLAPV.GSL.I.GWLALAL
RetrocopyASGTTLFCTSFYYQSLSGDHSIRTLAPVRGSLPIWGWLALAL

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 .38 RPM
SRP014902_testis 0 .14 RPM 23 .90 RPM
SRP018288_heart 0 .00 RPM 8 .54 RPM
SRP018288_kidney 0 .00 RPM 93 .68 RPM
SRP018288_liver 0 .00 RPM 17 .91 RPM
SRP018288_lung 0 .00 RPM 16 .90 RPM
SRP018856_adipose 0 .00 RPM 59 .12 RPM
SRP035408_brain 0 .06 RPM 6 .45 RPM
SRP035408_liver 0 .00 RPM 9 .78 RPM
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_160 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_160 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_160 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 22 parental genes, and 44 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000166835 retrocopies
Bos taurus ENSBTAG000000317523 retrocopies
Canis familiaris ENSCAFG000000232052 retrocopies
Callithrix jacchus ENSCJAG000000377861 retrocopy
Cavia porcellus ENSCPOG000000047601 retrocopy
Equus caballus ENSECAG000000164991 retrocopy
Echinops telfairi ENSETEG000000160763 retrocopies
Felis catus ENSFCAG000000298993 retrocopies
Homo sapiens ENSG000002055442 retrocopies
Gorilla gorilla ENSGGOG000000001132 retrocopies
Microcebus murinus ENSMICG000000125501 retrocopy
Macaca mulatta ENSMMUG000000156182 retrocopies
Mus musculus ENSMUSG000000703941 retrocopy
Nomascus leucogenys ENSNLEG000000094352 retrocopies
Otolemur garnettii ENSOGAG000000113781 retrocopy
Ochotona princeps ENSOPRG000000149782 retrocopies
Pongo abelii ENSPPYG000000079153 retrocopies
Pan troglodytes ENSPTRG000000309872 retrocopies
Pteropus vampyrus ENSPVAG000000050611 retrocopy
Rattus norvegicus ENSRNOG000000375402 retrocopies
Sus scrofa ENSSSCG00000025782 2 retrocopies
retro_sscr_160 , retro_sscr_330,
Tursiops truncatus ENSTTRG000000097942 retrocopies



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