RetrogeneDB ID:

retro_sscr_204

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:1:280470814..280471225(-)
Located in intron of:ENSSSCG00000005441
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CBX3
Ensembl ID:ENSSSCG00000016711
Aliases:None
Description:chromobox homolog 3 [Source:HGNC Symbol;Acc:1553]


Retrocopy-Parental alignment summary:






>retro_sscr_204
GTTGAAGAGGAAGAGCCTAGAGAATTTGTTGTAGAAAAAGTACTGGACCTATGTGTAGTGAATGGGAAAGTGGAATATTT
CTGAAAGTGCAAGGGGTTTACAGATGCAGACAATACTTGGGAATCTGATGAAAATCTGGATTGTTCAGAGTTAATTGAAG
CATTTCTTAATTCTCAAAAAGCTGGTAAAGAAAAAGATGGAACATAAAGAAAGTCATTATCTGACAGTGAATCTGATGAT
AGCAAATCAAAAAAAAGAAACACTGCTGATAAACCAAGAGGTTTTGCCAGAGGTCTTGATCCAGAACGAATAACTGGTGC
CACAGACAGCAGTGGAGAATTAATGTTTCTCAAGAAATGGAAAGATTCAGATGGGGCGGACTTGGTGGTGGCAAAAGAGG
AAAATATGAAG

ORF - retro_sscr_204 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.33 %
Parental protein coverage: 75.41 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLNSQKAGKEKDGAKR
VEE.EP.EFVVEKVLD..VVNGKVEYF.K.KGFTDADNTWE..ENLDC.ELIEAFLNSQKAGKEKDG..R
RetrocopyVEEEEPREFVVEKVLDLCVVNGKVEYF*KCKGFTDADNTWESDENLDCSELIEAFLNSQKAGKEKDGT*R
ParentalKSLSDSESDDSKSKKKRDAADKPRGFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMK
KSLSDSESDDSK.......ADKPRGFARGLDPERI.GATDSSGELMFL.KWKDSD.ADLV.AKE.NMK
RetrocopyKSLSDSESDDSK-XXXXNTADKPRGFARGLDPERITGATDSSGELMFLKKWKDSDGADLVVAKEENMK

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 7 .43 RPM
SRP014902_testis 0 .14 RPM 47 .81 RPM
SRP018288_heart 0 .00 RPM 55 .35 RPM
SRP018288_kidney 0 .00 RPM 64 .62 RPM
SRP018288_liver 0 .00 RPM 47 .33 RPM
SRP018288_lung 0 .00 RPM 96 .23 RPM
SRP018856_adipose 0 .00 RPM 16 .27 RPM
SRP035408_brain 0 .00 RPM 80 .67 RPM
SRP035408_liver 0 .00 RPM 52 .75 RPM
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_204 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_204 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_204 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 30 parental genes, and 182 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000059691 retrocopy
Canis familiaris ENSCAFG0000000289711 retrocopies
Choloepus hoffmanni ENSCHOG0000001384322 retrocopies
Callithrix jacchus ENSCJAG000000079528 retrocopies
Cavia porcellus ENSCPOG000000151681 retrocopy
Dasypus novemcinctus ENSDNOG0000000625019 retrocopies
Dipodomys ordii ENSDORG0000000548711 retrocopies
Equus caballus ENSECAG000000127801 retrocopy
Felis catus ENSFCAG000000152246 retrocopies
Homo sapiens ENSG000001225659 retrocopies
Gorilla gorilla ENSGGOG000000258536 retrocopies
Loxodonta africana ENSLAFG000000069073 retrocopies
Microcebus murinus ENSMICG0000000699811 retrocopies
Myotis lucifugus ENSMLUG000000075912 retrocopies
Mus musculus ENSMUSG000000298361 retrocopy
Nomascus leucogenys ENSNLEG000000149319 retrocopies
Otolemur garnettii ENSOGAG000000165831 retrocopy
Ochotona princeps ENSOPRG000000117139 retrocopies
Procavia capensis ENSPCAG000000049042 retrocopies
Pongo abelii ENSPPYG0000001771410 retrocopies
Pan troglodytes ENSPTRG0000001900310 retrocopies
Pteropus vampyrus ENSPVAG000000062972 retrocopies
Rattus norvegicus ENSRNOG000000118142 retrocopies
Sorex araneus ENSSARG000000080112 retrocopies
Sarcophilus harrisii ENSSHAG000000179131 retrocopy
Sus scrofa ENSSSCG00000016711 4 retrocopies
Sus scrofa ENSSSCG000000175291 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000062234 retrocopies
Tarsius syrichta ENSTSYG000000081596 retrocopies
Tursiops truncatus ENSTTRG000000007117 retrocopies



Copyright © RetrogeneDB 2014-2017