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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCAGGACGGAGGGGCTGCATCCTCGGGAGGCGGCTTCTTCTCGTCGTTCGCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttcggccacctgcttcctacctccccgctcctcccctcagatccgcatcgagctacccgttagagctctgcccgagctgatcgtggcctctcc...

Basic information

species Zea mays
transcript GRMZM2G174644_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174644_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 5'ss of exon 1
ACCAGGACGGAGGGGCTGCATCCTCGGGAGGCGGC------TTCTTCTCGTCGTTCGCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttcggccacctgcttcctacct-ccccgctcctcccctcagatccgcatcg----agctacccgttagagctctgcccgagctgatcgtggcctctcc
         | || || || || ||||||||||||      |||||||| ||| ||||||||||| ||||||||| |||||||||||| || ||||| |||||||||||||| |||  |||||  | ||   ||   | | |   | |   ||   |||   |     || | ||     ||||||  |||||  || ||    || |   
------GGAGTGGAGCCGCCTCGTCGGGAGGCGGCGGGGGCTTCTTCTCCTCGATCGCCGCCGGCGTGCGCAGCTTGGGCACCGCCGTCCACAAATCTGTCAACGGgtgagtcttcc-ccacccccctcgcgccggtctctcagttgcttgcaaccccgtgccctctcagatcccgacctgagctcc-cccgatttgttcacccccac---
















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|22491096|gb|BU051019.1|BU051019
EST:     CGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: CGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|19351392|gb|BM895924.1|BM895924
EST:     CGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGC-TGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: CGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|13150716|gb|BG321038.1|BG321038
EST:     CCGCCGGCATGCGCA-CTGGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: CCGCCGGCATGCGCAGCTGGGG-CACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|211272002|gb|FK970185.1|FK970185
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|74244334|gb|DT652248.1|DT652248
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|211271996|gb|FK970179.1|FK970179
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|211271998|gb|FK970181.1|FK970181
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|148954837|gb|EC900310.2|EC900310
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCGCAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|149078287|gb|EE167049.2|EE167049
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|71326510|gb|DR799932.1|DR799932
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCACCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|94475418|gb|EB704376.1|EB704376
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|148995971|gb|EE035219.2|EE035219
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|28909493|gb|CB331845.1|CB331845
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|76011657|gb|DT938827.1|DT938827
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|211272000|gb|FK970183.1|FK970183
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|211271999|gb|FK970182.1|FK970182
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|148940242|gb|EC885014.2|EC885014
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|78116426|gb|DV534813.1|DV534813
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|71326507|gb|DR799931.1|DR799931
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|211271997|gb|FK970180.1|FK970180
EST:     GCCGCCGGCATGCGCM--TGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTNAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|149084040|gb|EE173435.2|EE173435
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|211272003|gb|FK970186.1|FK970186
EST:     GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
EST: gi|18659308|gb|BM500269.1|BM500269
EST:     GCCGCCGGCATGCGCAN-TGGGGCACCGCCGTGCATAAATCCGTCAACGG                         GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA
genomic: GCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttc ... atgtctgtagGCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCAGGACGGAGGGGCTGCATCCTCGGGAGGCGGCTTCTTCTCGTCGTTCGCCGCCGGCATGCGCAGCTGGGGCACCGCCGTGCATAAATCCGTCAACGGgtgagttttcggccacctgcttcctacctccccgctcctcccctcagatccgcatcgagctacccgttagagctctgcccgagctgatcgtggcctctcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG