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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccctgttctgtctgaagcctttggtatgctgcacacgagcatttttttttttgaaaaatttgtgcagatcaattttgtttgcttgtggataaaacatagttataactttgaattttactttgccttgcttttcatacagATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGTTTGCATATTATGTCGGTGCTAGAAGCATCACCCCCAATACCGTCCCTGA

Basic information

species Zea mays
transcript GRMZM2G170868_T01
intron # 5
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|113702101|gb|EE679605.1|EE679605
EST:     GCTTCTGAGACAAATCAAGACAAGAAATGTTGGAGATGATGTTCGATCTG                         ATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGT
genomic: GCTTCTGAGACAAATCAAGACAAGAAATGTTGGAGATGATGTTCGATCTGgtaagccctg ... tttcatacagATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGT
EST: gi|78076529|gb|DV504963.1|DV504963
EST:     GCTTCTGAGACAAATCAAGACAAGAAATGTTGGAGATGATGTTCGATCTG                         ATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGT
genomic: GCTTCTGAGACAAATCAAGACAAGAAATGTTGGAGATGATGTTCGATCTGgtaagccctg ... tttcatacagATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGT
EST: gi|32835843|gb|CD975521.1|CD975521
EST:     GCTTCTGAGACAAATCAAGACAAGAAATGTTGGAGATGATGTTCGATCTG                         ATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGT
genomic: GCTTCTGAGACAAATCAAGACAAGAAATGTTGGAGATGATGTTCGATCTGgtaagccctg ... tttcatacagATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGT
EST: gi|149085411|gb|EE174917.2|EE174917
EST:     GCTTCTGAGACAAATCAAGACAAGAAATGTTGGAGATGATGTTCGATCTG                         ATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGT
genomic: GCTTCTGAGACAAATCAAGACAAGAAATGTTGGAGATGATGTTCGATCTGgtaagccctg ... tttcatacagATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGT
EST: gi|110200094|gb|EC881991.1|EC881991
EST:     GCTTCTGAGACAAATCAAGACAAGAAATGTTGGAGATGATGTTCGATCTG                         ATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGGCGTCACCATCTTAG
genomic: GCTTCTGAGACAAATCAAGACAAGAAATGTTGGAGATGATGTTCGATCTGgtaagccctg ... tttcatacagATTCTGAAGGAGAAGACGACCATGAAGACTGATT-GGCGTCACCATCTTAG
EST: gi|110200815|gb|EC882712.1|EC882712
EST:     GCTTCTGAGACAAATCAAGACAAGAAATGTTGGAGATGATGTTCGATCTG                         ATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGT
genomic: GCTTCTGAGACAAATCAAGACAAGAAATGTTGGAGATGATGTTCGATCTGgtaagccctg ... tttcatacagATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGT
EST: gi|211422774|gb|FL463571.1|FL463571
EST:     GCTTCTGAGACAAATCAAGACMAGAAATGTTGGAGATGATGTTCGATCTG                         ATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGT
genomic: GCTTCTGAGACAAATCAAGACAAGAAATGTTGGAGATGATGTTCGATCTGgtaagccctg ... tttcatacagATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGT
EST: gi|86465981|gb|DY232354.1|DY232354
EST:     GCTTCTGAGACAAATCAAGACAAGAAATGTTGGAGATGATGTTCGATCTG                         ATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGT
genomic: GCTTCTGAGACAAATCAAGACAAGAAATGTTGGAGATGATGTTCGATCTGgtaagccctg ... tttcatacagATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGT
EST: gi|14203683|gb|BG837360.1|BG837360
EST:     GATGATGTTCGATCTG                         ATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGT
genomic: GATGATGTTCGATCTGgtaagccctg ... tttcatacagATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGT
EST: gi|71756331|gb|DR954268.1|DR954268
EST:     GCTTCTGAGACAAATCAAGACAAGAAATGTTGGAGATGATGTTCGATCTG                         ATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGT
genomic: GCTTCTGAGACAAATCAAGACAAGAAATGTTGGAGATGATGTTCGATCTGgtaagccctg ... tttcatacagATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGT
EST: gi|211145609|gb|FL254132.1|FL254132
EST:     GCTTCTGAGACAAATCAAGACAAGAAATGTTGGAGATGATGTTCGATCTG                         ATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGT
genomic: GCTTCTGAGACAAATCAAGACAAGAAATGTTGGAGATGATGTTCGATCTGgtaagccctg ... tttcatacagATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGT
EST: gi|32935313|gb|CF040125.1|CF040125
EST:     GCTTCTGAGACAAATCAAGACAAGAAATGTTGGAGATGATGTTCGATCTG                         ATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGT
genomic: GCTTCTGAGACAAATCAAGACAAGAAATGTTGGAGATGATGTTCGATCTGgtaagccctg ... tttcatacagATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGT
EST: gi|211147030|gb|FL254134.1|FL254134
EST:     GCTTCTGAGACAAATCAAGACAAGAAATGTTGGAGATGATGTTCGATCTG                         ATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGT
genomic: GCTTCTGAGACAAATCAAGACAAGAAATGTTGGAGATGATGTTCGATCTGgtaagccctg ... tttcatacagATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggataaaacatagttataactttgaattttactttgccttgcttttcatacagATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGTTTGCATATTATGTCGGTGCTAGAAGCATCACCCCCAATACCGTCCCTGA
               ttataac  putative branch site (score: 2)
                            ttttactttgccttgc  putative PPT
     taaaacatagttataa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccctgttctgtctgaagcctttggtatgctgcacacgagcatttttttttttgaaaaatttgtgcagatcaattttgtttgcttgtggataaaacatagttataactttgaattttactttgccttgcttttcatacagATTCTGAAGGAGAAGACGACCATGAAGACTGATTGGCGTCACCATCTTAGTTTGCATATTATGTCGGTGCTAGAAGCATCACCCCCAATACCGTCCCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC