RetrogeneDB ID:

retro_opri_949

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_489:221188..222100(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DTWD1
Ensembl ID:ENSOPRG00000002951
Aliases:None
Description:DTW domain containing 1 [Source:HGNC Symbol;Acc:30926]


Retrocopy-Parental alignment summary:






>retro_opri_949
ATGTCTCTCAACTCACCTATATTTCTCGAAGAAAGTGAAGAAAGTAATTCAAAATTTGTGGAAACAAAACAGTCACAGAC
TACTTCCATAGCTTCAGAAGATCCCCTTCAGAACTTATGTTTAGCATCTCAAGAAGTTCTTCATAAAGCTCAACAAACTG
GGAGATCAAAGTGTCTACGATGTGGTGGTTCCAGAATGTTTTACTGCTATACATGTTATGTCCCAGTTGAAAATGTACCT
ATTGAACAGATTCCACTTGTGAAGCTTCCATTGAAGATCGACATCATTAAACATCCAAATGAAACAGATGGCAAAAGTAC
TGCTATACATGCAAAACTCTTAGCACCTGATTTTGTGAACATTTATACATATCCTTGTATTCCAGAATATGAAGAACAGG
ATTATGAAGTTGCGCTTATTTTTCCTGGACCTCAGTCTGTCTCCATAAAAGATATCTCTTTCCATCTACAAAAACGAATG
CAAGATAATATTAGAGACAAAAGTGATGACCCTGATAAGCCAACTGTTAAACGTAAAAAAACTGAAGAAATGGAGGACCT
TGATTTGATTGGCAGCAAGGGCAAAGGCACAATACTGAAAAAAATTATTTTTATAGATAGCACTTGGAACCAGACAAACA
AAATATTCACTGATGAGAGACTTCAAGGATTGTTACAAGTTGAGTTGAAAACAAGAAAAACTTGCTTTTGGCGCCATCAA
AAAGGAAAGCCAGACACTTTCCTTTCCACAATTGAAGCAATTTACTACTTTCTTGTGGACTACCATACTGAAATACTAAA
AGAGAAATACACAGGACAATATGACAATCTTTTATTTTTCTACTCCTTTATGTACAGGCTGATAAAGGATGCCAAATGCT
CTGGAGATAAAGAAAAAAGAAAACTTATCCAT

ORF - retro_opri_949 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.36 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSLNSPVFLEESEESNSKFVETKQSQTTSIASEDPLQNLCLASQEVLYKAQQTGRSKCLRCGGSRMFYCY
MSLNSP.FLEESEESNSKFVETKQSQTTSIASEDPLQNLCLASQEVL.KAQQTGRSKCLRCGGSRMFYCY
RetrocopyMSLNSPIFLEESEESNSKFVETKQSQTTSIASEDPLQNLCLASQEVLHKAQQTGRSKCLRCGGSRMFYCY
ParentalTCYVPVENVPIEQIPLVKLPLKIDIIKHPNETDGKSTAIHAKLLAPDFVNIYTYPCIPEYEEQDHEVALI
TCYVPVENVPIEQIPLVKLPLKIDIIKHPNETDGKSTAIHAKLLAPDFVNIYTYPCIPEYEEQD.EVALI
RetrocopyTCYVPVENVPIEQIPLVKLPLKIDIIKHPNETDGKSTAIHAKLLAPDFVNIYTYPCIPEYEEQDYEVALI
ParentalFPGPQSVSIKDISFHLQKRMQDNIRDKSDDPDKPTVKRKKTEEMEGLDLIGSKGKGTILKKIIFIDSTWD
FPGPQSVSIKDISFHLQKRMQDNIRDKSDDPDKPTVKRKKTEEME.LDLIGSKGKGTILKKIIFIDSTW.
RetrocopyFPGPQSVSIKDISFHLQKRMQDNIRDKSDDPDKPTVKRKKTEEMEDLDLIGSKGKGTILKKIIFIDSTWN
ParentalQTNKIFTDERLQGLLQVELKTRKTCFWRHQKGKPDTFLSTIEAIYYFLVDYHTEILKEKYTGQYDNLLFF
QTNKIFTDERLQGLLQVELKTRKTCFWRHQKGKPDTFLSTIEAIYYFLVDYHTEILKEKYTGQYDNLLFF
RetrocopyQTNKIFTDERLQGLLQVELKTRKTCFWRHQKGKPDTFLSTIEAIYYFLVDYHTEILKEKYTGQYDNLLFF
ParentalYSFMYRLIKDAKCSGDKEKRKLIH
YSFMYRLIKDAKCSGDKEKRKLIH
RetrocopyYSFMYRLIKDAKCSGDKEKRKLIH

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_949 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 10 parental genes, and 14 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000149261 retrocopy
Cavia porcellus ENSCPOG000000034612 retrocopies
Homo sapiens ENSG000001040471 retrocopy
Gorilla gorilla ENSGGOG000000279211 retrocopy
Nomascus leucogenys ENSNLEG000000061671 retrocopy
Otolemur garnettii ENSOGAG000000132911 retrocopy
Ochotona princeps ENSOPRG00000002951 2 retrocopies
retro_opri_136, retro_opri_949 ,
Pongo abelii ENSPPYG000000064642 retrocopies
Pan troglodytes ENSPTRG000000070581 retrocopy
Vicugna pacos ENSVPAG000000083582 retrocopies



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