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






RNA-Seq - click to see more details

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ochotona princeps was not studied using ChIP-Seq data.

EST - click to see more details

Ochotona princeps was not studied using EST data.

TSS - click to see more details

Ochotona princeps was not studied using FANTOM5 data.

Lab - click to see more details

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
retro_btau_114, retro_btau_115, retro_btau_192,
Canis familiaris ENSCAFG000000132491 retrocopy
retro_cfam_1007,
Equus caballus ENSECAG000000203632 retrocopies
retro_ecab_66, retro_ecab_93,
Equus caballus ENSECAG000000222601 retrocopy
retro_ecab_802,
Felis catus ENSFCAG0000003097714 retrocopies
retro_fcat_1021, retro_fcat_1388, retro_fcat_1569, retro_fcat_1683, retro_fcat_1825, retro_fcat_184, retro_fcat_1915, retro_fcat_220, retro_fcat_221, retro_fcat_334, retro_fcat_515, retro_fcat_566, retro_fcat_688, retro_fcat_737,
Homo sapiens ENSG0000015650827 retrocopies
retro_hsap_1093, retro_hsap_1181, retro_hsap_1567, retro_hsap_1671, retro_hsap_190, retro_hsap_2302, retro_hsap_2455, retro_hsap_2637, retro_hsap_2712, retro_hsap_278, retro_hsap_283, retro_hsap_2896, retro_hsap_2920, retro_hsap_2967, retro_hsap_2983, retro_hsap_3239, retro_hsap_3291, retro_hsap_3314, retro_hsap_363, retro_hsap_3701, retro_hsap_3706, retro_hsap_3758, retro_hsap_3825, retro_hsap_3917, retro_hsap_4220, retro_hsap_4730, retro_hsap_989,
Loxodonta africana ENSLAFG000000280811 retrocopy
retro_lafr_651,
Myotis lucifugus ENSMLUG0000001353724 retrocopies
retro_mluc_110, retro_mluc_1252, retro_mluc_1392, retro_mluc_1430, retro_mluc_1558, retro_mluc_1628, retro_mluc_1644, retro_mluc_1853, retro_mluc_1901, retro_mluc_1910, retro_mluc_2071, retro_mluc_2148, retro_mluc_2154, retro_mluc_2277, retro_mluc_2355, retro_mluc_2358, retro_mluc_2359, retro_mluc_2391, retro_mluc_441, retro_mluc_470, retro_mluc_677, retro_mluc_950, retro_mluc_956, retro_mluc_966,
Monodelphis domestica ENSMODG000000185334 retrocopies
retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Mustela putorius furoENSMPUG000000038166 retrocopies
retro_mputfur_1514, retro_mputfur_1643, retro_mputfur_220, retro_mputfur_502, retro_mputfur_844, retro_mputfur_862,
Mustela putorius furoENSMPUG0000000427110 retrocopies
retro_mputfur_1179, retro_mputfur_1276, retro_mputfur_1351, retro_mputfur_1394, retro_mputfur_284, retro_mputfur_355, retro_mputfur_474, retro_mputfur_678, retro_mputfur_920, retro_mputfur_973,
Oryctolagus cuniculus ENSOCUG000000084813 retrocopies
retro_ocun_1102, retro_ocun_187, retro_ocun_71,
Ochotona princeps ENSOPRG00000016685 6 retrocopies
retro_opri_1049, retro_opri_1076, retro_opri_1197 , retro_opri_298, retro_opri_325, retro_opri_383,
Sus scrofa ENSSSCG000000044894 retrocopies
retro_sscr_169, retro_sscr_492, retro_sscr_612, retro_sscr_758,
Tursiops truncatus ENSTTRG0000000011419 retrocopies
retro_ttru_1020, retro_ttru_1150, retro_ttru_1196, retro_ttru_1349, retro_ttru_1351, retro_ttru_1368, retro_ttru_1384, retro_ttru_1810, retro_ttru_1861, retro_ttru_1876, retro_ttru_384, retro_ttru_390, retro_ttru_401, retro_ttru_523, retro_ttru_664, retro_ttru_698, retro_ttru_844, retro_ttru_941, retro_ttru_998,
Drosophila melanogaster FBgn00005571 retrocopy
retro_dmel_9,


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