RetrogeneDB ID:

retro_ogar_2700

Retrocopy
location
Organism:Bushbaby (Otolemur garnettii)
Coordinates:GL873650.1:2248732..2249717(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:EI24
Ensembl ID:ENSOGAG00000001838
Aliases:None
Description:etoposide induced 2.4 [Source:HGNC Symbol;Acc:13276]


Retrocopy-Parental alignment summary:






>retro_ogar_2700
AAACCTTTCTCTAGGACCTTGCCCAGGGAATCCAAGACTCCATATGGGGTATTTGCACCATCTCAAAGTGAGATGCTTGT
TGAATCCATCAAAAGAGAGATGCGCCAGAGAAGACAGAGCAGCGTCCTAGCACAGAGGAGAGCCCAGAGGTCCGAGCGCA
AACAAGAGTGAGCTGCGTATTGTTGGTAGAATTTTCCAGGGTTGTGCTTGGAATGGTGGAGCATTCTGGTTTACTCTCTT
CTTTATCGAGTGTTTGTTCCTGTGCTTCCGTCAGTAACAGCCCCAGTTATCAGTGATCCATCACTACATGGAGACGTTTG
GTCACGGCTGGAATTCTTCCTAAAGTCAATTTTCAGCTCTCTCTAGGTGCTGCCATTTGCACTTCTCAGAGTTGTGAATG
CCCTCTGGTTTCCAGACATAGCTGCCCTGGCATGGGAGGCGTCAGGAAGAGAGCCCATCCACTCCCTGGTGTCAGCAGAA
TGACTGCTGACGTGCTTCTCAGCCCTTTGTTGCAGGCTCTTTTCCTTATCCCGGGAGTGCTCCTGAACCTCGTTTCTATC
TATCTTGATGGTCACCAGGTTAGTCTCCTTCATATGTCCCTTCTGGACTCACCGTATTGCTTAGAATATCATTCATTCAA
TAAAGGAATTGAAATACCCCAATGATTGTCAAACATAGGAAGGACCTGGCCTTACTACCTTGTCTGGGGTTTGCCTTTGG
CTTTTCTCAGGCAACACGGTCCTCACATCATCAGTGGCTGCCTCTCTCTATCCACTTTCCTTTATTCATTATCAGCACCA
GTGAAGCAAAGACACCTGAAAAGCGTACTTCTTCCAGCTGTGACTCTTCTCCTTGGTGGTCTCTTAAGCAACAGACTGTT
CCAGAAGACAGGGTACCTATAGTCTGCCCTGAGCAGCTCAGCCTTTGCAGAGAAGCTCCTTCACCACATTCCTCACCTGC
CAAACTGAAAGCCACTGAGGGCCAC

ORF - retro_ogar_2700 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 58.77 %
Parental protein coverage: 98.53 %
Number of stop codons detected: 4
Number of frameshifts detected 7


Retrocopy - Parental Gene Alignment:

ParentalKTFLQDLARGIKDSIWGICTISKLDARIQQKREEQRRRRASSVLAQRRAQSTERKQE-SEPRIVSRIFQC
K.F...L.R..K....G....S...........E.R.RR..S.....R..........SE.RIV.RIFQ.
RetrocopyKPFSRTLPRESKTP-YGVFAPSQSEMLVESIKREMRQRR-QSSVLAQRRAQRSERKQ>SELRIVGRIFQG
ParentalCAWNGGVFWCSL-LLFYRMFIPGLQYVTALIIGDPSLHGVFWSWLEFFLTSIFSALWVLPLFVLSKVVNA
CAWNGG.FW..L.LL.YR.F.P.L..VTA..I.DPSLHG..WS.LEFFL.SIFS.L.VLP.F.L..VVNA
RetrocopyCAWNGGAFWFTL<LL-YRVFVPVLPSVTAPVISDPSLHGDVWSRLEFFLKSIFSSL*VLP-FALLRVVNA
ParentalIWFQDIADLAFEVSGRRP-HPFPSVSKIIADMLFNLLLQALFLIQGMFVSLFPIHLVGQLVSLLHMSLLY
.WF.DIA.LA.E.SGR.P.HP.P.VS...AD.L...LLQALFLI.G....L..I.L.G..VSLLHMSLL.
RetrocopyLWFPDIAALAWEASGREP<HPLPGVSRMTADVLLSPLLQALFLIPGVLLNLVSIYLDGHQVSLLHMSLLD
ParentalSLYCFEYRWFNKGIEMHQRLSNIERNWPYYFGFGLPLAFLTAMQSSYIISGCL-FSILFPLFIISANEAK
S.YC.EY..FNKGIE..Q.LSNI.R.WPYY...GLPLAFL.......IISGCL..SI.FPLFIIS..EAK
RetrocopySPYCLEYHSFNKGIEIPQ*LSNIGRTWPYYLVWGLPLAFL-RQHGPHIISGCL<LSIHFPLFIISTSEAK
ParentalTPG-KAYLFQLRLFSLVV-FLSNRLFHKTVYLQSALSSSTSAETI-PSPHPSPAKPKAAAGH
TP..KAY.FQL.LFSLVV..LSNRLF.KT.YL.SALSSS..AE...PSPH.SPAK.KA..GH
RetrocopyTPE<KAYFFQL*LFSLVV<LLSNRLFQKTGYL*SALSSSAFAEKL<PSPHSSPAKLKATEGH

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Otolemur garnettii was not studied using ChIP-Seq data.

EST - click to see more details

Otolemur garnettii was not studied using EST data.

TSS - click to see more details

Otolemur garnettii was not studied using FANTOM5 data.

Lab - click to see more details

retro_ogar_2700 was not experimentally validated.

Retrocopy orthology:
Otolemur garnettii 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 26 parental genes, and 69 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000009902 retrocopies
retro_amel_1449, retro_amel_1681,
Bos taurus ENSBTAG000000072022 retrocopies
retro_btau_1242, retro_btau_443,
Canis familiaris ENSCAFG000000108981 retrocopy
retro_cfam_1829,
Choloepus hoffmanni ENSCHOG000000126693 retrocopies
retro_chof_1433, retro_chof_1994, retro_chof_804,
Cavia porcellus ENSCPOG000000072722 retrocopies
retro_cpor_132, retro_cpor_929,
Dasypus novemcinctus ENSDNOG000000023624 retrocopies
retro_dnov_1083, retro_dnov_1421, retro_dnov_2143, retro_dnov_2345,
Equus caballus ENSECAG000000158611 retrocopy
retro_ecab_1022,
Erinaceus europaeus ENSEEUG000000032741 retrocopy
retro_eeur_435,
Felis catus ENSFCAG000000151001 retrocopy
retro_fcat_1754,
Homo sapiens ENSG000001495473 retrocopies
retro_hsap_236, retro_hsap_2782, retro_hsap_3804,
Loxodonta africana ENSLAFG0000001088815 retrocopies
retro_lafr_262, retro_lafr_263, retro_lafr_264, retro_lafr_265, retro_lafr_394, retro_lafr_395, retro_lafr_396, retro_lafr_397, retro_lafr_398, retro_lafr_399, retro_lafr_566, retro_lafr_589, retro_lafr_626, retro_lafr_627, retro_lafr_999,
Microcebus murinus ENSMICG000000030233 retrocopies
retro_mmur_398, retro_mmur_498, retro_mmur_632,
Myotis lucifugus ENSMLUG000000015831 retrocopy
retro_mluc_1249,
Macaca mulatta ENSMMUG000000100093 retrocopies
retro_mmul_1443, retro_mmul_1653, retro_mmul_2244,
Nomascus leucogenys ENSNLEG000000074513 retrocopies
retro_nleu_2149, retro_nleu_684, retro_nleu_853,
Oryctolagus cuniculus ENSOCUG000000146701 retrocopy
retro_ocun_1578,
Otolemur garnettii ENSOGAG00000001838 6 retrocopies
retro_ogar_1055, retro_ogar_1379, retro_ogar_2700 , retro_ogar_2701, retro_ogar_659, retro_ogar_799,
Ochotona princeps ENSOPRG000000134912 retrocopies
retro_opri_106, retro_opri_1130,
Procavia capensis ENSPCAG000000127621 retrocopy
retro_pcap_452,
Pongo abelii ENSPPYG000000040333 retrocopies
retro_pabe_2234, retro_pabe_3107, retro_pabe_416,
Pan troglodytes ENSPTRG000000044444 retrocopies
retro_ptro_1202, retro_ptro_1883, retro_ptro_206, retro_ptro_2581,
Pteropus vampyrus ENSPVAG000000045321 retrocopy
retro_pvam_1124,
Rattus norvegicus ENSRNOG000000303911 retrocopy
retro_rnor_2605,
Sarcophilus harrisii ENSSHAG000000173331 retrocopy
retro_shar_433,
Ictidomys tridecemlineatus ENSSTOG000000042992 retrocopies
retro_itri_1343, retro_itri_1373,
Tarsius syrichta ENSTSYG000000047472 retrocopies
retro_tsyr_1238, retro_tsyr_1423,


Copyright © RetrogeneDB 2014-2017