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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattttcgatcattaagtgaagtatcaatctaagtatatgataattgctctgtgttaagataatacttgtattttatcctcatggtggttattgtggcagGGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATGTGGCACAGGCGTTGGAATACTGCAGTAGCAAAGGGAGGGCACTCTATCA

Basic information

species Zea mays
transcript GRMZM2G121826_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121826_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g61010.1 (Oryza sativa), 3'ss of exon 3
--tattttcgatcattaagtgaagtatcaatctaagtatatgataattgctctgtgttaagataatacttgtattttatcctcatggtggttattgt-ggcagGGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATGTGGCACAGGCGTTGGAATACTGCAGTAGCAAAGGGAGGGCACTCTATCA
     ||| |     |     |  || |  | | ||||   | ||    || ||  ||  |||  ||  |  |||||   ||||||||||||||  | ||||||||||||||| || ||||| ||||||||||||    | |||||||| |||||||| ||||| ||||| |||||||||||||||||||| || ||||| ||
agagcttttgcctcctgttgcatttaacgttttcagtaggag-tagacactttgcatttggat--tatctacattttgcgctcatggtggttatccttggcagGGGAGACAAAGCCATTGAGCTGGGCAATGAGGGTACGAGCTGCATTCTATGTGGCTCAGGCATTGGAGTACTGCAGTAGCAAAGGGAGAGCTCTCTACCA
















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|149103589|gb|EE288989.2|EE288989
EST:     CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACT                         GGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG
genomic: CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACTgtatgtttgg ... attgtggcagGGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG
EST: gi|71772711|gb|DR970638.1|DR970638
EST:     CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACT                         GGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG
genomic: CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACTgtatgtttgg ... attgtggcagGGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG
EST: gi|71302365|gb|DR787300.1|DR787300
EST:     CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACT                         GGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG
genomic: CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACTgtatgtttgg ... attgtggcagGGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG
EST: gi|91055451|gb|EB165869.1|EB165869
EST:     CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACT                         GGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG
genomic: CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACTgtatgtttgg ... attgtggcagGGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG
EST: gi|67034938|gb|CO463471.1|CO463471
EST:     CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACT                         GGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG
genomic: CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACTgtatgtttgg ... attgtggcagGGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG
EST: gi|149012049|gb|EE042465.2|EE042465
EST:     CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACT                         GGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG
genomic: CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACTgtatgtttgg ... attgtggcagGGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG
EST: gi|149102733|gb|EE188271.2|EE188271
EST:     CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTTCACT                         GGGAGACAAATCCGTTGAGTTGGGGCA-TGAGGACGAGGGCTGCATTTTAT
genomic: CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACTgtatgtttgg ... attgtggcagGGGAGACAAATCCGTTGAGTTGGG-CAATGAGGACGAGGGCTGCATTTTAT
EST: gi|211227820|gb|FL399533.1|FL399533
EST:     CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTTCACT                         GGGAGACAAATCCCGT-GAGTTGGGCAAT
genomic: CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACTgtatgtttgg ... attgtggcagGGGAGACAAATCC-GTTGAGTTGGGCAAT
EST: gi|211332705|gb|FL418379.1|FL418379
EST:     CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACT                         GGGAGACAAATCCCGTTGAGTTGGGCAATGAGGACGAAGGCTGGATTTTAT
genomic: CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACTgtatgtttgg ... attgtggcagGGGAGACAAATCC-GTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTAT
EST: gi|18659368|gb|BM500301.1|BM500301
EST:     CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACT                         GGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG
genomic: CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACTgtatgtttgg ... attgtggcagGGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG
EST: gi|71327655|gb|DR800438.1|DR800438
EST:     CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACT                         GGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG
genomic: CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACTgtatgtttgg ... attgtggcagGGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG
EST: gi|71299876|gb|DR785964.1|DR785964
EST:     CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACT                         GGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG
genomic: CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACTgtatgtttgg ... attgtggcagGGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG
EST: gi|148982427|gb|EE028311.2|EE028311
EST:     CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACT                         GGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG
genomic: CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACTgtatgtttgg ... attgtggcagGGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG
EST: gi|149036971|gb|EE155209.2|EE155209
EST:     CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACT                         GGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG
genomic: CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACTgtatgtttgg ... attgtggcagGGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG
EST: gi|211443081|gb|FL371156.1|FL371156
EST:     CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACT                         GGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTCTATG
genomic: CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACTgtatgtttgg ... attgtggcagGGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG
EST: gi|148945740|gb|EC891020.2|EC891020
EST:     CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACT                         GGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG
genomic: CGTCGCCGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTTTTCCACTgtatgtttgg ... attgtggcagGGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctctgtgttaagataatacttgtattttatcctcatggtggttattgtggcagGGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATGTGGCACAGGCGTTGGAATACTGCAGTAGCAAAGGGAGGGCACTCTATCA
         ttaagataatacttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattttcgatcattaagtgaagtatcaatctaagtatatgataattgctctgtgttaagataatacttgtattttatcctcatggtggttattgtggcagGGGAGACAAATCCGTTGAGTTGGGCAATGAGGACGAGGGCTGCATTTTATGTGGCACAGGCGTTGGAATACTGCAGTAGCAAAGGGAGGGCACTCTATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG