RetrogeneDB ID:

retro_opri_1197

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_9326:4016..4877(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:EEF1A1
Ensembl ID:ENSOPRG00000016685
Aliases:None
Description:eukaryotic translation elongation factor 1 alpha 1 [Source:HGNC Symbol;Acc:3189]


Retrocopy-Parental alignment summary:






>retro_opri_1197
GTCAGGGAATTTGAAGCTGGTATCTCCAAGAATGGGAAGGCCCATGAGTATATCCTTCTGGCTTATACCCTGGGTCTGAA
ACAACTAATCATAGGTGTTAACACAATGGATTCCACTGAACCACCCTACAGCCTGAAGAGATACAAGGAAATTCTTAAGG
AAGTCGGCACCTACATTAAGAAAACTGGCTACAACCCTGACACAGTACATTTGTACCAGTTTGGAACAGTGACAACATGC
TGGAGCCAAGTGCTAATATGATGTAGTTTAAGGGATGGAAAATCACCCACAAAGACGGCAATGCCAGTGGAATCACACTG
CTAGAAACCCTGGATTGCATCCTCCACCAACAAGACCAACCAATTAGTCTCTGCATCTGCCCCTGCAAGATGTCTACAAA
ATTGTTGGTATTGGCACTGTGCCTGTAGGCCGAGTGGAGGCTGGTGTTCTGGAACCTAGCATGGTGGTAACCTTTGCTCC
TGTCATCACAACCAAAGTCAAGTCTGTTGAAATGCACCACGAAGCTTTGTGTGAAGCCATTCCTGGTGACAATGGGAGCT
TCAAAATCAAGAACATGTCAGTCAAAGATGTTCATAGTGGCAATGTGGCTGGTGACAGCAAAAATGACCCACCAATGCAG
GCAGCTGGATTTACTGCTCAGGTAATCATCCTGAATCATCCAAGTCAAGTCATTGCTGGCCAACCCCTGTGCTGAATTGT
CACCCAGCTTGCTTGTTTGCAGAGCTGAAGGGAAAGATTGATCATCGTTCTAGAAAGAAGCAGGAAGATGGCCCTAAATT
CCTGAAATCTGGTGATGCTGCCACTGTTGACATGGTCCCTGGTAAATCCATGTGTTGAGAG

ORF - retro_opri_1197 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.44 %
Parental protein coverage: 63.64 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalVGEFEAGISKNGQTREHALLAYTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTV-
V.EFEAGISKNG...E..LLAYTLG.KQLI.GVN.MDSTEPPYS.KRY.EI.KEV.TYIKK.GYNPDTV.
RetrocopyVREFEAGISKNGKAHEYILLAYTLGLKQLIIGVNTMDSTEPPYSLKRYKEILKEVGTYIKKTGYNPDTV<
ParentalAFVPISGWNGDNMLEPSANMPWFKGWKVTRKDGNASGTTLLEALDCIL-PPTRPTDKPLRLPLQDVYKIG
.FVP...WN.DNMLEPSANM..FKGWK.T.KDGNASG.TLLE.LDCIL.PPTRPT...L.LPLQDVYKI.
RetrocopyTFVPV--WNSDNMLEPSANMM*FKGWKITHKDGNASGITLLETLDCIL<PPTRPTN*SLHLPLQDVYKIV
ParentalGIGTVPVGRVETGVLKPGMVVTFAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAG
GIGTVPVGRVE.GVL.P.MVVTFAPV..TT.VKSVEMHHEAL.EA.PGDN..F..KN.SVKDV..GNVAG
RetrocopyGIGTVPVGRVEAGVLEPSMVVTFAPV-ITTKVKSVEMHHEALCEAIPGDNGSFKIKNMSVKDVHSGNVAG
ParentalDSKNDPPMEAAGFTAQVIILNHPGQISAGY-APVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKS
DSKNDPPM.AAGFTAQVIILNHP.Q..AG...PVL.CH.A...C.FAELK.KID.RS.KK.EDGPKFLKS
RetrocopyDSKNDPPMQAAGFTAQVIILNHPSQVIAGQ<TPVLNCHPA---CLFAELKGKIDHRSRKKQEDGPKFLKS
ParentalGDAAIVDMVPGKPMCVE
GDAA.VDMVPGK.MC.E
RetrocopyGDAATVDMVPGKSMC*E

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_1197 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 16 parental genes, and 126 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000145343 retrocopies
Canis familiaris ENSCAFG000000132491 retrocopy
Equus caballus ENSECAG000000203632 retrocopies
Equus caballus ENSECAG000000222601 retrocopy
Felis catus ENSFCAG0000003097714 retrocopies
Homo sapiens ENSG0000015650827 retrocopies
Loxodonta africana ENSLAFG000000280811 retrocopy
Myotis lucifugus ENSMLUG0000001353724 retrocopies
Monodelphis domestica ENSMODG000000185334 retrocopies
Mustela putorius furoENSMPUG000000038166 retrocopies
Mustela putorius furoENSMPUG0000000427110 retrocopies
Oryctolagus cuniculus ENSOCUG000000084813 retrocopies
Ochotona princeps ENSOPRG00000016685 6 retrocopies
Sus scrofa ENSSSCG000000044894 retrocopies
Tursiops truncatus ENSTTRG0000000011419 retrocopies
Drosophila melanogaster FBgn00005571 retrocopy



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