RetrogeneDB ID:

retro_ogar_682

Retrocopy
location
Organism:Bushbaby (Otolemur garnettii)
Coordinates:GL873525.1:21620056..21621207(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SMARCE1
Ensembl ID:ENSOGAG00000001652
Aliases:None
Description:SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 [Source:HGNC Symbol;Acc:11109]


Retrocopy-Parental alignment summary:






>retro_ogar_682
ATGTCAAAAAGACCATCATTCGTCCCATCTCCCACCCCAGCTCCTGCAACACAAATGCCCAACACACCAAGGTTTGTGGG
ATACAATCCATACAGTCATCTCGCCTACAACAATTATAGGCTGGGAGGAAACCTGGACACACAGGTCACGGCATCCTCTG
GTATTACATTCCCCAAACCCCCAAAGCCACCAGATAAGCCACTGATGCCCTACATGAGGTACAGCAGAAAGGTCTGGGAC
CAAGTAAAGGCTTGTAACCCTGACCTATAGTTGTGGGAGATTAACAAGATTATTGGTGGCATGTGGCGAAATCTCACTGA
TGAAGAGAAACAAGAATATTTAAATGAATATGAAGCAGAAAAAAGAGAATGCAATGAATCTATGAAGGCCTATCATAATT
CTGCTGCATACCTTGCTTACAGAAATCCAAAAAGTCGTGCAGAAGTTGCTTTAGAGGAAGAGTCAGAGACAGTCGACAGA
GACAGTCTCGTATGGAGAAAAGAGAACCTTACATGAACATTCAGCCTCCTGAAGATCCAGATGATTATGATGATGGCTTT
TCAATGAAGCATACAGCCGCCGCCCGTTTCCAGAGAAACCACCACCTCATTAGCGAAATCCTTAGCGAGAATGTGGTGCC
AGACGTTGGGCCAGTTGTCACAACAGCTAGGATGCTGGTCCTCAAATGGCAGGTCCAGTCTTTAATGGTCATCAGCAAAA
ACTAGAAGCTGAACTTCTTCAATAGAGGGACGACATCAAGAAAAGAAAGGGAAATCTCTGGAAAGCACAGATTCATTTAA
CAATGGACTTAAAAGGTCGTGCTGTCTGAAGGTAAGTGGATATGGTGAAGATTGCCGCCGAGATCGCGCAGGCAGAGAGA
GGAGCAGGCCTGCAGAGGCAGGAGGCCGCCGAGCAGGTGGAGCACAGGCAGAGCAGCGTGGTTTCCAGCAGGAGTAAACG
GCCAGCAAAGCTGAGGCAAAGAAAGAGGGTGAGAACGTTCCGATAGAGACAGAGGAGACACACCTCGAAGAAATGACAGC
AAGCCGGAAGAATGGAGTAGAAGGCACAACTCCTGAAGACAAGGAGAGTGGGCAGGAGGGGTCAACAGTATGGCCGAGGA
AGGAACCAGTGAGAGCAACAGTGCCACAGAG

ORF - retro_ogar_682 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.04 %
Parental protein coverage: 94.89 %
Number of stop codons detected: 2
Number of frameshifts detected: 4


Retrocopy - Parental Gene Alignment:

ParentalMSKRPSYAPPPTPAPATQMPSTPGFVGYNPYSHLAYNNYRLGGNPGTNSRVTASSGITIPKPPKPPDKPL
MSKRPS..P.PTPAPATQMP.TP.FVGYNPYSHLAYNNYRLGGN..T...VTASSGIT.PKPPKPPDKPL
RetrocopyMSKRPSFVPSPTPAPATQMPNTPRFVGYNPYSHLAYNNYRLGGNLDT--QVTASSGITFPKPPKPPDKPL
ParentalMPYMRYSRKVWDQVKASNPDLKLWEIGKIIGGMWRDLTDEEKQEYLNEYEAEKIEYNESMKAYHNSPAYL
MPYMRYSRKVWDQVKA.NPDL.LWEI.KIIGGMWR.LTDEEKQEYLNEYEAEK.E.NESMKAYHNS.AYL
RetrocopyMPYMRYSRKVWDQVKACNPDL*LWEINKIIGGMWRNLTDEEKQEYLNEYEAEKRECNESMKAYHNSAAYL
ParentalAYINAKSRAEAALEEES-RQRQSRMEKGE---PYMSIQPAEDPDDYDDGFSMKHTATARFQRNHRLISEI
AY.N.KSRAE.ALEEES.R....R....E...PYM.IQP.EDPDDYDDGFSMKHTA.ARFQRNH.LISEI
RetrocopyAYRNPKSRAEVALEEES<RDSRQRQSRMEKREPYMNIQPPEDPDDYDDGFSMKHTAAARFQRNHHLISEI
ParentalLSESVVPDVRSVVTTARMQVLKRQVQSLMV-HQRKLEAELLQ-IEERHQEKKRKFLESTDSFNNELKRLC
LSE.VVPDV..VVTTARM.VLK.QVQSLMV.HQ.KLEAELLQ.IE.RHQEKK.K.LESTDSFNN.LKR.C
RetrocopyLSENVVPDVGPVVTTARMLVLKWQVQSLMV<HQQKLEAELLQ<IEGRHQEKKGKSLESTDSFNNGLKRSC
ParentalGLKVEVDMEKIAAEIAQAEEQARKRQEEREKEAAEQAERSQSSIVPEEEQAASKAEEKKDDENIPMETEE
.LKV....E......A..E...R.R..E.....A..A...Q.....E.......A...K..EN.P.ETEE
RetrocopyCLKVSGYGEDCRRDRAGRE---RSRPAEAGGRRAGGAQAEQRGFQQE*TASKAEAK--KEGENVPIETEE
ParentalTHLEETTESQQNGEEGTSTPDDKESGQE-GVDSMAEEGTSDSNTGSE
THLEE.T.S..NG.EGT.TP.DKESGQE.GV.SMAEEGTS.SN...E
RetrocopyTHLEEMTASRKNGVEGT-TPEDKESGQE<GVNSMAEEGTSESNSATE

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_682 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 17 parental genes, and 68 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000135734 retrocopies
retro_cjac_1107, retro_cjac_2109, retro_cjac_50, retro_cjac_854,
Homo sapiens ENSG000000735845 retrocopies
retro_hsap_1195, retro_hsap_1304, retro_hsap_3623, retro_hsap_3947, retro_hsap_922,
Gorilla gorilla ENSGGOG000000118032 retrocopies
retro_ggor_1020, retro_ggor_931,
Microcebus murinus ENSMICG000000098214 retrocopies
retro_mmur_1408, retro_mmur_1592, retro_mmur_608, retro_mmur_928,
Myotis lucifugus ENSMLUG000000046091 retrocopy
retro_mluc_1209,
Macaca mulatta ENSMMUG000000040053 retrocopies
retro_mmul_1284, retro_mmul_2159, retro_mmul_2286,
Mustela putorius furoENSMPUG000000146604 retrocopies
retro_mputfur_1411, retro_mputfur_1482, retro_mputfur_1499, retro_mputfur_739,
Mus musculus ENSMUSG000000379355 retrocopies
retro_mmus_1111, retro_mmus_1127, retro_mmus_2437, retro_mmus_2618, retro_mmus_3194,
Nomascus leucogenys ENSNLEG000000019574 retrocopies
retro_nleu_1060, retro_nleu_2051, retro_nleu_2083, retro_nleu_286,
Oryctolagus cuniculus ENSOCUG000000089811 retrocopy
retro_ocun_59,
Otolemur garnettii ENSOGAG00000001652 7 retrocopies
retro_ogar_1734, retro_ogar_2059, retro_ogar_3199, retro_ogar_402, retro_ogar_454, retro_ogar_682 , retro_ogar_760,
Ochotona princeps ENSOPRG000000009851 retrocopy
retro_opri_731,
Pongo abelii ENSPPYG000000084564 retrocopies
retro_pabe_2973, retro_pabe_3251, retro_pabe_794, retro_pabe_994,
Pan troglodytes ENSPTRG000000229025 retrocopies
retro_ptro_2451, retro_ptro_2678, retro_ptro_3039, retro_ptro_639, retro_ptro_894,
Pteropus vampyrus ENSPVAG000000113551 retrocopy
retro_pvam_237,
Rattus norvegicus ENSRNOG000000106767 retrocopies
retro_rnor_1278, retro_rnor_1311, retro_rnor_1456, retro_rnor_1507, retro_rnor_1599, retro_rnor_2383, retro_rnor_2593,
Tupaia belangeri ENSTBEG0000000077010 retrocopies
retro_tbel_1246, retro_tbel_1554, retro_tbel_2208, retro_tbel_2955, retro_tbel_4035, retro_tbel_4629, retro_tbel_4656, retro_tbel_658, retro_tbel_821, retro_tbel_844,


Copyright © RetrogeneDB 2014-2017