RetrogeneDB ID:

retro_tbel_3628

Retrocopy
location
Organism:Treeshrew (Tupaia belangeri)
Coordinates:scaffold_147257:100968..101849(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSTBEG00000013044
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_tbel_3628
GGCCCTCCCAGTGGGCCAGGCTCAGAGGTGTGGGGGATGCCCCGTCTCCCTAACTGTGTGAGTTCTACGGGGGGATGGCT
TACGGTGGACCTCCGGTGGGAGCAGGGTTACCGCCCTAAGCTAGCCTTAAGACCCCCAAACTCAGGGTGAGGGGAGCCCG
GCTGGAGAGCAACTCTGAGGGAGCCTCCCAGCCCTCACTGCCCCTCCTGGTGGCATGAAGCTGAAGTTGGAGCAAATCCC
CAAGAAGCCCCAGGATGTCAAAGCTCTGCAGGAAGAGCTCGAACAATTTGCCAAGCTCCGGAAGCAGAAGAGGGCCACTG
GGATATACCCAGACTGGCCTGGGCCCACCCCAGGGTTCTCTTTAGGGAGGGGTCTGGCCAAACGACTTCTGCCGCGGGAG
GCTCTTCAGCTCAGGTTCCAAAACACGTGCAGACCTCAGCCCTGCTGCGGGAGTGGCCTGAGGAGCTGACAATGAGAATC
TTCAGGAGACATGCGAAGCGGAGACCTGGTGCAGACCCGAGAGAGAGACTGAAGGAGGCTGAGAACCGAGAACCTCGTGA
GAGGCGTCTGGAGAGCCCATTCCTGCAGTCCCAAATCCGCACTGCGGCAGGTCAGCCTCGGCACCCAGCTTTGACTTGAG
AAGGTTGTGGTCCGAGCGTGGTTCTGGAACGGGTGCCAGATGGGCCAGGGATCAGGCGGTGACTCTTCACAAGGCTTTGA
GGCTGCTGGGCCTCTTTTCTCAGACCAGCATCCTTTCCCCAGGGCCCCATTTGGGTACCCCAGGCTACGGGAGCCCTCAC
GTCAGGAAACCCCACACTCCTCCGTCCCTTTCCCTGCCCAGAAGCCTTCGCTCTGTCTCTGCCACCACACTGGGCTCTCC
T

ORF - retro_tbel_3628 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 52.5 %
Parental protein coverage: 85.75 %
Number of stop codons detected: 4
Number of frameshifts detected 11


Retrocopy - Parental Gene Alignment:

ParentalGPGVGPGSEMWGIP-PCPPPYEFCGGMAYCGPSVGVGLVPSNNLEMSQLEVEVGAGEERNSEEAS-PECA
GP..GPGSE.WG.P.P.P...EF.GGMAY.GP.VG.GL.P...L....L.V..GA..E.NSE.AS.P...
RetrocopyGPPSGPGSEVWGMP<PSP*LCEFYGGMAYGGPPVGAGLPP*ASLKTPKLRVR-GARLESNSEGAS<PALT
ParentalAPLADLKLEESLEQNPEKSQDIEALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRF
AP....KL...LEQ.P.K.QD..ALQ.ELEQFAKL.KQKR.T.G......G.T.G...G.........R.
RetrocopyAPPGGMKLK--LEQIPKKPQDVKALQEELEQFAKLRKQKRAT-GIYPDWPGPTPGFSLGRGLAKRLLPR-
ParentalEALQLSFKNMCKLRP-LLQKWVEE-ADNNENLQEICKAET-LVQARKR--KRTSIENRVRG-NLENMFLQ
EALQL.F.N.C...P.LL..W.EE.AD.NENLQE.C.AET.LVQ.R.R...R...EN.VRG..LE..FLQ
RetrocopyEALQLRFQNTCRPQP<LLREWPEE<AD-NENLQETCEAET<LVQTRERD*RRLRTENLVRG<RLESPFLQ
Parental-CPKP-TLQQIGHIAQQLGLEKDVVRVWFCNRRQKGKRSSSDYVQREDFEAAGSPFSGGPVPFPLAPGPH
..P.P..L.Q......QL.LEK.VVR.WF.N..Q.G..S..D......FEAAG..FS....PFP.AP...
Retrocopy<VPNP<ALRQVS-LGTQL*LEKVVVRAWFWNGCQMGQGSGGD--SSQGFEAAGPLFS-DQHPFPRAP---
ParentalFG-TPGYGSPHFTSLYSSV-PFPEGEAFP-PVSVTTLGSP
FG.TPGYGSPH.........PFP..EAF...VS.TTLGSP
RetrocopyFG>TPGYGSPHVRKPHTPP>PFPCPEAFA<SVSATTLGSP

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






RNA-Seq - click to see more details

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Tupaia belangeri was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_tbel_3628 retrocopy.

TSS - click to see more details

Tupaia belangeri was not studied using FANTOM5 data.

Lab - click to see more details

retro_tbel_3628 was not experimentally validated.

Retrocopy orthology:
Tupaia belangeri 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 25 parental genes, and 63 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000103773 retrocopies
retro_amel_1057, retro_amel_1213, retro_amel_1616,
Bos taurus ENSBTAG000000211112 retrocopies
retro_btau_1576, retro_btau_951,
Canis familiaris ENSCAFG000000004851 retrocopy
retro_cfam_1538,
Callithrix jacchus ENSCJAG000000197891 retrocopy
retro_cjac_123,
Dipodomys ordii ENSDORG000000095491 retrocopy
retro_dord_65,
Equus caballus ENSECAG000000089671 retrocopy
retro_ecab_301,
Erinaceus europaeus ENSEEUG000000153572 retrocopies
retro_eeur_196, retro_eeur_558,
Felis catus ENSFCAG000000010783 retrocopies
retro_fcat_1372, retro_fcat_1422, retro_fcat_275,
Gorilla gorilla ENSGGOG000000276623 retrocopies
retro_ggor_2275, retro_ggor_295, retro_ggor_852,
Macropus eugenii ENSMEUG000000132213 retrocopies
retro_meug_1146, retro_meug_1475, retro_meug_692,
Microcebus murinus ENSMICG000000015111 retrocopy
retro_mmur_1423,
Myotis lucifugus ENSMLUG000000110283 retrocopies
retro_mluc_1465, retro_mluc_2382, retro_mluc_515,
Mustela putorius furoENSMPUG000000012022 retrocopies
retro_mputfur_253, retro_mputfur_96,
Mus musculus ENSMUSG000000244062 retrocopies
retro_mmus_2201, retro_mmus_250,
Oryctolagus cuniculus ENSOCUG000000171603 retrocopies
retro_ocun_1175, retro_ocun_1696, retro_ocun_463,
Otolemur garnettii ENSOGAG000000006213 retrocopies
retro_ogar_1406, retro_ogar_1436, retro_ogar_2229,
Ochotona princeps ENSOPRG000000039262 retrocopies
retro_opri_1213, retro_opri_556,
Pongo abelii ENSPPYG000000172103 retrocopies
retro_pabe_2761, retro_pabe_3294, retro_pabe_898,
Pan troglodytes ENSPTRG000000179535 retrocopies
retro_ptro_1798, retro_ptro_204, retro_ptro_2132, retro_ptro_2721, retro_ptro_733,
Pteropus vampyrus ENSPVAG000000073342 retrocopies
retro_pvam_724, retro_pvam_74,
Rattus norvegicus ENSRNOG000000464874 retrocopies
retro_rnor_1474, retro_rnor_2186, retro_rnor_2968, retro_rnor_921,
Sus scrofa ENSSSCG000000013932 retrocopies
retro_sscr_252, retro_sscr_678,
Ictidomys tridecemlineatus ENSSTOG000000261033 retrocopies
retro_itri_1076, retro_itri_1705, retro_itri_951,
Tupaia belangeri ENSTBEG00000013044 4 retrocopies
retro_tbel_3628 , retro_tbel_3718, retro_tbel_3779, retro_tbel_4614,
Tarsius syrichta ENSTSYG000000073404 retrocopies
retro_tsyr_1508, retro_tsyr_1630, retro_tsyr_814, retro_tsyr_817,


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