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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCAGTGTCAAAGACATTTGCAAAGATGGCGGCATATTCAAGAAGATCCTTAAAGAGGGAGAGAAATGGGAGAACCCAAAGGATCCTGATGAAGTACTTGgtaatttttttgcttattgcgacacttttcatagagctgatttatttggttcctataacttatactctccttgctcttgtag

Basic information

species Zea mays
transcript GRMZM2G096585_T05
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G096585_T05 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g41390.2 (Oryza sativa), 5'ss of exon 3
ACCAGTGTCAAAGACATTTGCAAAGATGGCGGCATATTCAAGAAGATCCTTAAAGAGGGAGAGAAATGGGAGAACCCAAAGGATCCTGATGAAGTACTTGgtaatttttttgcttattgcgacacttttcatagagctgatttatttggttcctataacttatactctccttgctcttgtag
|| |||||||| ||||||||| ||||||| || |||||||||||||| || || |||||||| ||||||||||||||||| |||| |||||||||| |||||||| |||  ||| ||||  |||  || |    | || || ||||     ||| || || |  || | | |  |  |||||
ACAAGTGTCAAGGACATTTGCCAAGATGGTGGTATATTCAAGAAGATACTGAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTGgtaatattt--gctcattgaaacatattgct---atcttatatattg---ccctgtagctgaccctttgcat--tgctgtag
















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|148938868|gb|EC883219.2|EC883219
EST:     TAAAGAGGGAGAGAAATGGGAGAACCCAAAGGATCCTGATGAAGTACTTG                         TGAAATATGAGGCCCGTCTGGAAGATGGTACTGTTGTATCCAAGTCTGAGG
genomic: TAAAGAGGGAGAGAAATGGGAGAACCCAAAGGATCCTGATGAAGTACTTGgtaatttttt ... gctcttgtagTGAAATATGAGGCCCGTCTGGAAGATGGTACTGTTGTATCCAAGTCTGAGG
EST: gi|211437295|gb|FL195681.1|FL195681
EST:     AAAGAGGGAGAGAAATGGGGAGAACCCAAAGGATCCTGATGAAGTACTTG                         TGAAATATGAGGCCCGTCTGGAAGAATGGTACTGTTGTATCCAAGTCGGAA
genomic: AAAGAGGGAGAGAAATGGG-AGAACCCAAAGGATCCTGATGAAGTACTTGgtaatttttt ... gctcttgtagTGAAATATGAGGCCCGTCTGGAAGA-TGGTACTGTTGTATCCAAGTCTGA-
EST: gi|211437302|gb|FL195688.1|FL195688
EST:     TAAAGAGGGAGAGAAATGGGAGAACCCAAAGGATCCTGATGAAGTACTTG                         TGAAATATTGAG-CCCGTCTGGGAGATGGTACTGNTGTATCCAAGTCTGAA
genomic: TAAAGAGGGAGAGAAATGGGAGAACCCAAAGGATCCTGATGAAGTACTTGgtaatttttt ... gctcttgtagTGAAATAT-GAGGCCCGTCTGGAAGATGGTACTGTTGTATCCAAGTCTGA-
EST: gi|148961764|gb|EE012538.2|EE012538
EST:     TAAAGAGGGAGAGAAATGGGAGAACCCAAAGGATCCTGATGAAGTACTTG                         TGAAATATGAGGCCCGTCTGGAAGATGGGACTGTTGTATCCAAGTCTGAGG
genomic: TAAAGAGGGAGAGAAATGGGAGAACCCAAAGGATCCTGATGAAGTACTTGgtaatttttt ... gctcttgtagTGAAATATGAGGCCCGTCTGGAAGATGGTACTGTTGTATCCAAGTCTGAGG
EST: gi|211429499|gb|FL195642.1|FL195642
EST:     AAAGAGGGAGAGAAATGGGAGAACCCCAAAG-ATCCTGATGAAGTACTTG                         TGAAATATGAGGCCCGGTCTGGAAGATGGGACTGTTTGTATCCAAGTCTGA
genomic: AAAGAGGGAGAGAAATGGGAGAACCC-AAAGGATCCTGATGAAGTACTTGgtaatttttt ... gctcttgtagTGAAATATGAGGCCCG-TCTGGAAGATGGTACTGTT-GTATCCAAGTCTGA
EST: gi|149111770|gb|EE190920.2|EE190920
EST:     TAAAGAGGGAGAGAAATGGGAGAACCCAAAGGATCCTGATGAAGTACTTG                         TGAAATATGAGGCCCGTCTGGAAGATGGTACTGTTGTATCCAAGTCTGAGG
genomic: TAAAGAGGGAGAGAAATGGGAGAACCCAAAGGATCCTGATGAAGTACTTGgtaatttttt ... gctcttgtagTGAAATATGAGGCCCGTCTGGAAGATGGTACTGTTGTATCCAAGTCTGAGG
EST: gi|71767511|gb|DR965448.1|DR965448
EST:     TAAAGAGGGAGAGAAATGGGAGAACCCAAAGGATCCTGATGAAGTACTTG                         TGAAATATGAGGCCCGTCTGGAAGATGGTACTGTTGTATCCAAGTCTGAGG
genomic: TAAAGAGGGAGAGAAATGGGAGAACCCAAAGGATCCTGATGAAGTACTTGgtaatttttt ... gctcttgtagTGAAATATGAGGCCCGTCTGGAAGATGGTACTGTTGTATCCAAGTCTGAGG
EST: gi|47962115|gb|CN844824.1|CN844824
EST:     TAAAGAGGGAGAGAAATGGGAGAACCCAAAGGATCCTGATGAAGTACTTG                         TGAAATATGAGGCCCGTCTGGAAGATGGTACTGTTGTATCCAAGTCTGAGG
genomic: TAAAGAGGGAGAGAAATGGGAGAACCCAAAGGATCCTGATGAAGTACTTGgtaatttttt ... gctcttgtagTGAAATATGAGGCCCGTCTGGAAGATGGTACTGTTGTATCCAAGTCTGAGG
EST: gi|149081119|gb|EE170223.2|EE170223
EST:     TAAAGAGGGAGAGAAATGGGAGAACCCAAAGGATCCTGATGAAGTACTTG                         TGAAATATGAGGCCCGTCTGGAAGATGGTACTGTTGTATCCAAGTCTGAGG
genomic: TAAAGAGGGAGAGAAATGGGAGAACCCAAAGGATCCTGATGAAGTACTTGgtaatttttt ... gctcttgtagTGAAATATGAGGCCCGTCTGGAAGATGGTACTGTTGTATCCAAGTCTGAGG
EST: gi|148958573|gb|EC904817.2|EC904817
EST:     TAAAGAGGGAGAGAAATGGGAGAACCCAAAGGATCCTGATGAAGTACTTG                         TGAAATATGAGGCCCGTCTGGAAGATGGTACTGTTGTATCCAAGTCTGAGG
genomic: TAAAGAGGGAGAGAAATGGGAGAACCCAAAGGATCCTGATGAAGTACTTGgtaatttttt ... gctcttgtagTGAAATATGAGGCCCGTCTGGAAGATGGTACTGTTGTATCCAAGTCTGAGG
EST: gi|149009170|gb|EE041295.2|EE041295
EST:     TAAAGAGGGAGAGAAATGGGAGAACCCAAAGGATCCTGATGAAGTACTTG                         TGAAATATGAGGCCCGTCTGGAAGATGGTACTGTTGTATCCAAGTCTGAGG
genomic: TAAAGAGGGAGAGAAATGGGAGAACCCAAAGGATCCTGATGAAGTACTTGgtaatttttt ... gctcttgtagTGAAATATGAGGCCCGTCTGGAAGATGGTACTGTTGTATCCAAGTCTGAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCAGTGTCAAAGACATTTGCAAAGATGGCGGCATATTCAAGAAGATCCTTAAAGAGGGAGAGAAATGGGAGAACCCAAAGGATCCTGATGAAGTACTTGgtaatttttttgcttattgcgacacttttcatagagctgatttatttggttcctataacttatactctccttgctcttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA