RetrogeneDB ID:

retro_opri_578

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_18067:78769..79174(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:AGPAT2
Ensembl ID:ENSOPRG00000003291
Aliases:None
Description:1-acylglycerol-3-phosphate O-acyltransferase 2 [Source:HGNC Symbol;Acc:325]


Retrocopy-Parental alignment summary:






>retro_opri_578
ATCATCAGTTGGTTTGTGCGGACCTTCAAGTACGTGTATAGCCTCCGCTTTGAGGTCAGGGGCTGGCCCAAGCTGGACAT
CGACTAGCCCTGCGTCATCATCTCCAACCGCCAGAGTATCCTGGACATGATGGGCCTCATGGAGGTCCTGCCATGGCGCT
GCGTGCAGGTAGCCAAGTGGGAGCTCCTGTTCCTGGGCTCCATGAGACTCATCATGTACCTGAGTGGCGTCTTCTTCAAG
AGTCGACAGCAGTCCAGCACCGCCATGAGTGTTCTGGCCAGCCTGAGCGAGCGCATGGTCCTGGAGAACCTCAAAGTGTG
GATCTACCCTGAGGGCACGTGCAACACCAATGGTGACCTACTGCCCTGCAGGAAAGGTGGTTTAAGGATGGCATTCATTG
AACAG

ORF - retro_opri_578 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80. %
Parental protein coverage: 63.08 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalIISWFVRTFKYMYGLRFEVRGQPKLDVDQPCVIISNHQSILDMMGLMEVLPRRCVQVAKRELLFLGPVGL
IISWFVRTFKY.Y.LRFEVRG.PKLD.D.PCVIISN.QSILDMMGLMEVLP.RCVQVAK.ELLFLG...L
RetrocopyIISWFVRTFKYVYSLRFEVRGWPKLDID*PCVIISNRQSILDMMGLMEVLPWRCVQVAKWELLFLGSMRL
ParentalIMYLGGVFFINRQQSSTAMSVMADLSERMVRENLKVWIYPEGTRNTNGDLLPFKKGAFYLAIQAQ
IMYL.GVFF..RQQSSTAMSV.A.LSERMV.ENLKVWIYPEGT.NTNGDLLP..KG....A...Q
RetrocopyIMYLSGVFFKSRQQSSTAMSVLASLSERMVLENLKVWIYPEGTCNTNGDLLPCRKGGLRMAFIEQ

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_578 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 8 parental genes, and 9 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000039651 retrocopy
Canis familiaris ENSCAFG000000195691 retrocopy
Equus caballus ENSECAG000000109321 retrocopy
Felis catus ENSFCAG000000116071 retrocopy
Myotis lucifugus ENSMLUG000000073482 retrocopies
Mustela putorius furoENSMPUG000000112491 retrocopy
Ochotona princeps ENSOPRG00000003291 1 retrocopy
retro_opri_578 ,
Ictidomys tridecemlineatus ENSSTOG000000234221 retrocopy



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