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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAAGGAGTAGATCGTCGACCCAGAACCCTCGCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgctgggacttgggatcgatttttatctgcgggtggtagttgttgatgctatgcctgctgcatgcgggatttgtcagacccttgcgaattagca...

Basic information

species Zea mays
transcript GRMZM2G093050_T04
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G093050_T04 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g03070.1 (Oryza sativa), 5'ss of exon 2
GAGAAGGAGTAGATCGTCGACCCAGA-----ACCCTCGCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgctgggacttgggatcgatt---tttatctgcgggtggtagttgttgatgctatgcctgctgcatgcgggatttgtcagacccttgcgaattagca---
      | ||||||||    |  |||     | || ||   |||||||| ||||||||||||||||||||||| |||||||| || |||||||  |     ||| |||||  ||   ||||| |  |||    |||| |   || | ||   ||         ||   |   |    |||     |  |    
------GTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtccc-----ctttggatctgttatgtttatttagggg-accagttttcactgttttgtaagcatggaattcgaaaagagcggtgtttgattcctcccgtca
















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|211266101|gb|FL146502.1|FL146502
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
EST: gi|211263664|gb|FL146490.1|FL146490
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
EST: gi|211266099|gb|FL146500.1|FL146500
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
EST: gi|211266096|gb|FL146497.1|FL146497
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
EST: gi|211268539|gb|FL146518.1|FL146518
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
EST: gi|67019799|gb|CO448548.1|CO448548
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
EST: gi|211268535|gb|FL146514.1|FL146514
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
EST: gi|211266094|gb|FL146495.1|FL146495
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
EST: gi|211268533|gb|FL146512.1|FL146512
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
EST: gi|211268537|gb|FL146516.1|FL146516
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
EST: gi|211268530|gb|FL146509.1|FL146509
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
EST: gi|211266093|gb|FL146494.1|FL146494
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
EST: gi|211266095|gb|FL146496.1|FL146496
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
EST: gi|211268531|gb|FL146510.1|FL146510
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
EST: gi|211266105|gb|FL146506.1|FL146506
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
EST: gi|211268534|gb|FL146513.1|FL146513
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
EST: gi|211268536|gb|FL146515.1|FL146515
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
EST: gi|211266100|gb|FL146501.1|FL146501
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
EST: gi|211266092|gb|FL146493.1|FL146493
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
EST: gi|148930736|gb|EC873025.2|EC873025
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
EST: gi|211268529|gb|FL146508.1|FL146508
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
EST: gi|211266097|gb|FL146498.1|FL146498
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
EST: gi|211263666|gb|FL146492.1|FL146492
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
EST: gi|149076177|gb|EE164770.2|EE164770
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
EST: gi|101389305|gb|EB816607.1|EB816607
EST:     GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG                         AATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC
genomic: GCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgct ... tttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAAGGAGTAGATCGTCGACCCAGAACCCTCGCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAGgtgagttgctgggacttgggatcgatttttatctgcgggtggtagttgttgatgctatgcctgctgcatgcgggatttgtcagacccttgcgaattagca

- - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA