RetrogeneDB ID:

retro_sscr_703

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:3:62296416..62296709(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL34
Ensembl ID:ENSSSCG00000009146
Aliases:None
Description:ribosomal protein L34 [Source:HGNC Symbol;Acc:10340]


Retrocopy-Parental alignment summary:






>retro_sscr_703
GTCCAGCATTTGACAAATCATCATAAGCTGTCCTACAGTACAGCCTCTACCAAAACTAAGCTGTCCCAAACCCCTGCTAA
CAGAATTGTTTACCTTTACACCGCAAAGTCAAGGAGAGTACCAGAATCTGCACGTGGCCTGTGCCCAGGCTGACTTTGAG
AAGTTTCTACTTGGAGACCTAAACTTCTTATGAGGTTGTCAAAAATGAAAGATCATATCAGCAGGGCTTATGGTGGTTGC
AGTCTGCTAAATGTTTCCATGACAGGATAGAGCATGACTTCTTTACTGAGGAA

ORF - retro_sscr_703 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 60.61 %
Parental protein coverage: 83.76 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalVQRLTYRRRLSYNTASNKTRLSRTPGNRIVYLYTKKVGKAPKSACGVCPGRLRGVRAVRPKVLMRLSKTK
VQ.LT....LSY.TAS.KT.LS.TP.NRIVYLYT.K....P.SA.G.CPG.L..V...RPK.LMRLSK.K
RetrocopyVQHLTNHHKLSYSTASTKTKLSQTPANRIVYLYTAKSRRVPESARGLCPG*L*EVSTWRPKLLMRLSKMK
ParentalKHVSRAYGGS-MCAKCVRDRIKRAFLIEE
.H.SRAYGG....AKC..DRI...F..EE
RetrocopyDHISRAYGGC<QSAKCFHDRIEHDFFTEE

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 100 .88 RPM
SRP014902_testis 0 .00 RPM 599 .73 RPM
SRP018288_heart 0 .00 RPM 233 .25 RPM
SRP018288_kidney 0 .00 RPM 294 .53 RPM
SRP018288_liver 0 .00 RPM 280 .48 RPM
SRP018288_lung 0 .00 RPM 321 .06 RPM
SRP018856_adipose 0 .00 RPM 673 .61 RPM
SRP035408_brain 0 .00 RPM 263 .77 RPM
SRP035408_liver 0 .00 RPM 204 .49 RPM
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_703 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_703 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_703 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 14 parental genes, and 88 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG0000001117926 retrocopies
Equus caballus ENSECAG000000197191 retrocopy
Gadus morhua ENSGMOG000000099821 retrocopy
Loxodonta africana ENSLAFG000000326156 retrocopies
Macropus eugenii ENSMEUG000000093613 retrocopies
Myotis lucifugus ENSMLUG000000004644 retrocopies
Monodelphis domestica ENSMODG000000206013 retrocopies
Pelodiscus sinensis ENSPSIG000000032951 retrocopy
Sarcophilus harrisii ENSSHAG000000013571 retrocopy
Sarcophilus harrisii ENSSHAG000000020523 retrocopies
Sus scrofa ENSSSCG00000009146 8 retrocopies
Tupaia belangeri ENSTBEG0000000357424 retrocopies
Tursiops truncatus ENSTTRG000000034436 retrocopies
Xenopus tropicalis ENSXETG000000210951 retrocopy



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