RetrogeneDB ID:

retro_tbel_1500

Retrocopy
location
Organism:Treeshrew (Tupaia belangeri)
Coordinates:GeneScaffold_4895:474955..476137(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:EIF4A2
Ensembl ID:ENSTBEG00000002268
Aliases:None
Description:eukaryotic translation initiation factor 4A2 [Source:HGNC Symbol;Acc:3284]


Retrocopy-Parental alignment summary:






>retro_tbel_1500
GGCCCCGATGGAATGGAGCCCGATGGCTTCATCGAGAGTAACTGGAACGAGATTGTTGACAGCTTTGATGACATGAACCT
CTCAGTGTCCCTTCTCCGTGGCATCTATGCCTATGGTTTTGAGAAACCCTCTGCCATCCAGCAGCGAGCCATTCTTCCTT
GTATCAAGGGTTGTGATGTGATTGCTCAAGCCCAGTCTGGGACTAGGAAAATGGCCACATTTGCCAAATCGATTTTGCAG
CAGATTGAATTAGATCTAAAGGCCATCCAGGCTTTGGTCCTGGCACCCACTCGAGAATTGGCTCAACAGATACAGAAGAT
GGTCATGGCACTCGGGAACTACATGGGTGCCTCCTGTCATGCCTGCATTGGGGGCACCAATGTGCATGCTGAGGTGCAGA
AGCTACAAATGGAAGCTCCCCACGTCATTGTGGGTACTCCTGGCTGCGTGTTTGATTTGCTTAACCAGAGATACCTGTCT
CCCAAATACATCAAGATGTTTGTATTGGATGAAGCTGACGAGATGTTAAGCCATGGATTCAGGGACCAGATCTATGACAT
ATTCCAAAAGCTCAATAGCAACACTCAGGTGATTTTGCTGTCAGCTACAATGCCTTCTGATGTGCTTGAGGTGACCAAGA
AGTTCATGAAGGACCCTATTCGGATTCTTTTCAAGAAGGAACAGTTGACCCTGGAGGGTATCCATCAGTTCTACATCAAT
GTGGAATGAGAGGAGTGGAAGCTGGACATGCTGTGTGACTTGTATGAAACCCTGACCATCACCCAGGCGGTCATCTTCAT
CAACACCCGAAGGAAGGTGGATTGGCTCACTGAGAAGTCGCATGCCCGAGACTTCACTGTGTCTGCCATGCATGGTGATA
TGGACCAAAAGGAACGAGATATAATCATGAGGGAGTTCCGTTCTGGCTCTAGCAGAGTATTGATTACTACTGACCTGCTG
GCCAGTGGCATCAATGTGCAACAAGTTTCTTTAGTCATCAACTATGACCTTCCCACCAACAGGGAAAACTGTATCCACAG
AATCGGCTATGGTGGACAATTTGGCCGTAAAGACGTGGCTATTAACATGGTGACAGAGGAAGACAAGAGGACTCTATGAG
ACATTGAGACCTTCTACAATACCACCATTGAGGAGAAGCCCCTCAGTGTTGCTGACCTCATC

ORF - retro_tbel_1500 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.76 %
Parental protein coverage: 99.24 %
Number of stop codons detected: 2
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalGSEGMDPDGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGK
G..GM.PDG.IESNWNEIVD.FDDMNL..SLLRGIYAYGFEKPSAIQQRAI.PCIKG.DVIAQAQSGT.K
RetrocopyGPDGMEPDGFIESNWNEIVDSFDDMNLSVSLLRGIYAYGFEKPSAIQQRAILPCIKGCDVIAQAQSGTRK
ParentalTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAP
.ATFA.SILQQ.E...K..QALVLAPTRELAQQIQK...ALG.YMGA.CHACIGGTNV..E.QKLQ.EAP
RetrocopyMATFAKSILQQIELDLKAIQALVLAPTRELAQQIQKMVMALGNYMGASCHACIGGTNVHAEVQKLQMEAP
ParentalHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLE
H..VGTPG.VFD.LN.RYLSPK.IKMFVLDEADEMLS.GF.DQIY.IFQKLN...QV.LLSATMP.DVLE
RetrocopyHVIVGTPGCVFDLLNQRYLSPKYIKMFVLDEADEMLSHGFRDQIYDIFQKLNSNTQVILLSATMPSDVLE
ParentalVTKKFMRDPIRILVKKEELTLEGIKQFYINVEREEWKLDTLCDLYETLTITQAVIFLNTRRKVDWLTEKM
VTKKFM.DPIRIL.KKE.LTLEGI.QFYINVE.EEWKLD.LCDLYETLTITQAVIF.NTRRKVDWLTEK.
RetrocopyVTKKFMKDPIRILFKKEQLTLEGIHQFYINVE*EEWKLDMLCDLYETLTITQAVIFINTRRKVDWLTEKS
ParentalHARDFTVSALHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGR
HARDFTVSA.HGDMDQKERD.IMREFRSGSSRVLITTDLLA.GI.VQQVSLVINYDLPTNREN.IHRIG.
RetrocopyHARDFTVSAMHGDMDQKERDIIMREFRSGSSRVLITTDLLASGINVQQVSLVINYDLPTNRENCIHRIGY
ParentalGGRFGRKGVAINFVTEEDKRILRDIETFYNTTVEEMPMNVADLI
GG.FGRK.VAIN.VTEEDKR.L.DIETFYNTT.EE.P..VADLI
RetrocopyGGQFGRKDVAINMVTEEDKRTL*DIETFYNTTIEEKPLSVADLI

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_1500 retrocopy.

TSS - click to see more details

Tupaia belangeri was not studied using FANTOM5 data.

Lab - click to see more details

retro_tbel_1500 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 21 parental genes, and 49 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000147242 retrocopies
retro_btau_258, retro_btau_522,
Canis familiaris ENSCAFG000000136591 retrocopy
retro_cfam_378,
Cavia porcellus ENSCPOG000000111831 retrocopy
retro_cpor_639,
Dasypus novemcinctus ENSDNOG000000115025 retrocopies
retro_dnov_1264, retro_dnov_2018, retro_dnov_2066, retro_dnov_648, retro_dnov_869,
Echinops telfairi ENSETEG000000185653 retrocopies
retro_etel_1174, retro_etel_2164, retro_etel_451,
Homo sapiens ENSG000001569762 retrocopies
retro_hsap_593, retro_hsap_878,
Gorilla gorilla ENSGGOG000000058672 retrocopies
retro_ggor_525, retro_ggor_712,
Macropus eugenii ENSMEUG000000117371 retrocopy
retro_meug_237,
Microcebus murinus ENSMICG000000073771 retrocopy
retro_mmur_525,
Macaca mulatta ENSMMUG000000037022 retrocopies
retro_mmul_1055, retro_mmul_2450,
Nomascus leucogenys ENSNLEG000000066331 retrocopy
retro_nleu_2589,
Oryctolagus cuniculus ENSOCUG000000050113 retrocopies
retro_ocun_392, retro_ocun_696, retro_ocun_763,
Otolemur garnettii ENSOGAG000000107292 retrocopies
retro_ogar_2830, retro_ogar_943,
Ochotona princeps ENSOPRG000000041701 retrocopy
retro_opri_498,
Pongo abelii ENSPPYG000000143842 retrocopies
retro_pabe_596, retro_pabe_677,
Pan troglodytes ENSPTRG000000157181 retrocopy
retro_ptro_437,
Rattus norvegicus ENSRNOG000000018152 retrocopies
retro_rnor_1163, retro_rnor_2340,
Ictidomys tridecemlineatus ENSSTOG000000126011 retrocopy
retro_itri_858,
Tupaia belangeri ENSTBEG00000002268 11 retrocopies
retro_tbel_114, retro_tbel_1488, retro_tbel_1500 , retro_tbel_2048, retro_tbel_2524, retro_tbel_2729, retro_tbel_2733, retro_tbel_3159, retro_tbel_3793, retro_tbel_4599, retro_tbel_841,
Takifugu rubripes ENSTRUG000000056602 retrocopies
retro_trub_14, retro_trub_6,
Tarsius syrichta ENSTSYG000000130503 retrocopies
retro_tsyr_1905, retro_tsyr_903, retro_tsyr_935,


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