RetrogeneDB ID:

retro_opri_103

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_231:171631..172156(-)
Located in intron of:ENSOPRG00000003547
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CBX3
Ensembl ID:ENSOPRG00000011713
Aliases:None
Description:chromobox homolog 3 [Source:HGNC Symbol;Acc:1553]


Retrocopy-Parental alignment summary:






>retro_opri_103
CAAAAAATGGGAAAGAAGCAGAATGGAAAGAGCAAAAAGGTCGAAGAAGCAGAGCCTGAAGAGTTTGTGGTGGAGAAGGT
GTTGGACCACCGTGTGGTCAATGGGAAGGTGGAGTACTTTCTGAAGTGGAAGGAATTCACAGATGCTGACACCACTTGGG
AACCTGAAGAAAATCTAGATTGTCCAGAGTTAATTGAAGCATTTCTTAATTCTCAAAAAGCTGGTAAAGAAAAAGATGGT
GCCAAAAGAAAATCCTTATCTGACAGTGAATCTGATGCCAGTAAATCAAAGAAGAAAAGAGATGCTGCTGACAAACCGAG
GGGCTTTGCCAGGGGTCTTGATCCTGAACGAATAATTGGTGCCACAGATAGCAGTGGGGAGTTGATGTTTCTCATGAAGT
GGAAAGATTCAGATGGAGCTGACTTGGTGCTGGCAAAAGAAGCAAATATGAAATGTCCTCGGATTGTAATTGCTTTTTAT
GAAGAGGGACCAACTTGGCATTCTTGTCCGGAAGATGAAGCTCAG

ORF - retro_opri_103 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.43 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalQKMGKKQNGKSKKVEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLN
QKMGKKQNGKSKKVEEAEPEEFVVEKVLD.RVVNGKVEYFLKWK.FTDAD.TWEPEENLDCPELIEAFLN
RetrocopyQKMGKKQNGKSKKVEEAEPEEFVVEKVLDHRVVNGKVEYFLKWKEFTDADTTWEPEENLDCPELIEAFLN
ParentalSQKAGKEKDGAKRKSLSDSESDDSKSKKKRDAADKPRGFARGLDPERIIGATDSSGELMFLMKWKDSDEA
SQKAGKEKDGAKRKSLSDSESD.SKSKKKRDAADKPRGFARGLDPERIIGATDSSGELMFLMKWKDSD.A
RetrocopySQKAGKEKDGAKRKSLSDSESDASKSKKKRDAADKPRGFARGLDPERIIGATDSSGELMFLMKWKDSDGA
ParentalDLVLAKEANMKCPQIVIAFYEERLTWHSCPEDEAQ
DLVLAKEANMKCP.IVIAFYEE..TWHSCPEDEAQ
RetrocopyDLVLAKEANMKCPRIVIAFYEEGPTWHSCPEDEAQ

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Ochotona princeps was not studied using RNA-Seq expression data.
Ochotona princeps was not studied using ChIP-Seq data.
Ochotona princeps was not studied using EST data.
Ochotona princeps was not studied using FANTOM5 data.
retro_opri_103 was not experimentally validated.

Retrocopy orthology:
Ochotona princeps does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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 ENSOPRG000000036991 retrocopy
Ochotona princeps ENSOPRG00000011713 9 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 ENSSSCG000000167114 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000062234 retrocopies
Tarsius syrichta ENSTSYG000000081596 retrocopies
Tursiops truncatus ENSTTRG000000007117 retrocopies



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