RetrogeneDB ID:

retro_opri_553

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_16931:22156..22678(-)
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:ENSOPRG00000003507
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_opri_553
ATGGGTAAAGGAGACCCCAACAAGCCGAGGGGCAAGATGTCCTCCTACGCCTTCTTCGTGCAGACGTGCCGGGAGGAGCA
CAAGAAGAAGCATCCGGACTCCTCGGTCAACTTCGCCGAGTTCTCGAAGAAATGCTCGGAGAGATGGAAGACCCTGTCTG
CCAAGGAGAAGTCCAAGTTTGAAGACATGGCCAAAAGCGATAAAGCGCGCTATGACCGGGAGATGAAAAATTACGTCCCC
CCCAAAGGCGACAAGAAGGGAAAGAAGAAAGATCCCAATGCTCCCAAGAGACCGCCATCTGCCTTCTTCCTGTTTTGCTC
TGAACATCGTCCAAAGATCAAAAGCGAACACCCAGGGCTGTCCATTGGGGATACTGCAAAGAAATTGGGTGAGATGTGGT
CTGAACAGTCAGCCAAAGATAAACAGCCCTACGAACAGAAGGCAGCTAAGCTAAAGGAGAAGTATGAAAAGGATATTGCT
GCATACCGTGCCAAGGGCAAGAGTGAAGCAGGAAAGAAGGGT

ORF - retro_opri_553 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.16 %
Parental protein coverage: 80.75 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKAR
MGKGDP.KPRGKMSSYAFFVQTCREEHKKKHPD.SVNF.EFSKKCSERWKT.SAKEK.KFEDMAK.DKAR
RetrocopyMGKGDPNKPRGKMSSYAFFVQTCREEHKKKHPDSSVNFAEFSKKCSERWKTLSAKEKSKFEDMAKSDKAR
ParentalYEREMKTYIPPKGETKKKFKDPNAPKRPPSDFFLFCSEYRPKIK-EHPGLSIGDMAKKLGEM-CNTAADD
Y.REMK.Y.PPKG..K.K.KDPNAPKRPPS.FFLFCSE.RPKIK.EHPGLSIGD.AKKLGEM.....A.D
RetrocopyYDREMKNYVPPKGDKKGKKKDPNAPKRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKD
ParentalKQPYEXXXXXXXXXXXXDIAAYRAKGKPDAAKKG
KQPYE............DIAAYRAKGK..A.KKG
RetrocopyKQPYEQKAAKLKEKYEKDIAAYRAKGKSEAGKKG

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_553 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 15 parental genes, and 180 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG0000000659713 retrocopies
Choloepus hoffmanni ENSCHOG0000000242316 retrocopies
Homo sapiens ENSG0000018940337 retrocopies
Gorilla gorilla ENSGGOG0000002676423 retrocopies
Loxodonta africana ENSLAFG000000002694 retrocopies
Macropus eugenii ENSMEUG000000013802 retrocopies
Macaca mulatta ENSMMUG000000233993 retrocopies
Monodelphis domestica ENSMODG0000000923814 retrocopies
Ochotona princeps ENSOPRG00000003507 8 retrocopies
Procavia capensis ENSPCAG000000022012 retrocopies
Pongo abelii ENSPPYG0000000554635 retrocopies
Pteropus vampyrus ENSPVAG000000014316 retrocopies
Rattus norvegicus ENSRNOG000000298131 retrocopy
Sorex araneus ENSSARG0000000447014 retrocopies
Sarcophilus harrisii ENSSHAG000000140342 retrocopies



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