RetrogeneDB ID:

retro_opri_20

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_1032:246595..247061(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RAB6B
Ensembl ID:ENSOPRG00000001164
Aliases:None
Description:RAB6B, member RAS oncogene family [Source:HGNC Symbol;Acc:14902]


Retrocopy-Parental alignment summary:






>retro_opri_20
TCAGAGACAATGTTTTTGGAGGATAGAAAAGCCAGGCTAATGTGTGGAATGCTGTGGATCAGGCACATGTTCATAGCCTC
ATTCCCAGTGACATCCTTGATTCTTTTGCAAGTATAGTAGTTCACAATATTACAAATGTTAATGGCTTCCAGCAAACTCC
AAAATGGGTTGATAATATCAGAACAGAAAGAGGAAATGATGATATCATCATGCTAGCACAAATTAAAACAGATCTTGTTG
ACAAGAAGCAAGTTTCTACTGAGGAGAGAAAGAGAAAAGCCAATGAGCTAAATGCCATGTTTATTGAAACTAGTGAGAAA
GCAAAATAAATGTAAAGAAGCTCTTCTGACTTGTGGCAACAGCTTTGCCTGGAATAGAAAACACACAGGACAGAATGAGG
AAAGATATGATTAACATAAACCTGGAAAAGCCTCAGGTCCAGCCAGTCAGCAAATGCTGTTCCTGC

ORF - retro_opri_20 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 54.72 %
Parental protein coverage: 75.48 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalSKTMYLEDRTVRLQ-LWDTAGQERFRSLIPSYIRDSTVAVVVYDITNLNSFQQTSKWIDDVRTERGSDVI
S.TM.LEDR..RL...W....Q....SLIPS.I.DS....VV..ITN.N.FQQT.KW.D..RTERG.D.I
RetrocopySETMFLEDRKARLM<VWNAVDQAHVHSLIPSDILDSFASIVVHNITNVNGFQQTPKWVDNIRTERGNDDI
ParentalIMLVGNKTDLADKRQITIEEGEQRAKELSVMFIETSAK-TGYNVKQLFRRVASALPGMENVQEKSKEGMI
IML...KTDL.DK.Q...EE....A.EL..MFIETS.K....NVK.LF..VA.ALPG.EN.Q......MI
RetrocopyIMLAQIKTDLVDKKQVSTEERKRKANELNAMFIETSEK<SKINVKKLF*LVATALPGIENTQDRMRKDMI
ParentalDIKLDKPQEPPASEGGCSC
.I.L.KPQ..P.S...CSC
RetrocopyNINLEKPQVQPVSK-CCSC

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_20 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 6 parental genes, and 17 retrocopies.

Species Parental gene accession Retrocopies number
Echinops telfairi ENSETEG000000094121 retrocopy
Loxodonta africana ENSLAFG000000099051 retrocopy
Ornithorhynchus anatinus ENSOANG000000316231 retrocopy
Ochotona princeps ENSOPRG00000001164 5 retrocopies
Ochotona princeps ENSOPRG000000103556 retrocopies
Pongo abelii ENSPPYG000000036633 retrocopies



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