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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAATGTTGTTTGGAGCTCAGTGACACCATCTTGTAATGCCTGTGATTTTACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCATgtaagtgttggtatttatgctgtcaagaccttaaaccctaaacctgtgtctgtttgccataccacagatagttagctcattagctagcctatatatgtag

Basic information

species Zea mays
transcript GRMZM2G040349_T01
intron # 2
splice site 5'
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|211338110|gb|FL126023.1|FL126023
EST:     TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCAT                         GGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
genomic: TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCATgtaagtgttg ... atatatgtagGGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
EST: gi|211338111|gb|FL126024.1|FL126024
EST:     TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCAT                         GGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
genomic: TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCATgtaagtgttg ... atatatgtagGGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
EST: gi|149028984|gb|EE286170.2|EE286170
EST:     TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCAT                         GGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
genomic: TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCATgtaagtgttg ... atatatgtagGGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
EST: gi|89762792|gb|DY690244.1|DY690244
EST:     TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCAT                         GGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
genomic: TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCATgtaagtgttg ... atatatgtagGGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
EST: gi|211340500|gb|FL126029.1|FL126029
EST:     TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCAT                         GGCTCCTTGTCAGGAAATGGTTACGAGATGAAACATTCAGGCCATAAAGTT
genomic: TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCATgtaagtgttg ... atatatgtagGGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
EST: gi|211340498|gb|FL126027.1|FL126027
EST:     TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCAT                         GGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
genomic: TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCATgtaagtgttg ... atatatgtagGGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
EST: gi|211338112|gb|FL126025.1|FL126025
EST:     TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCAT                         GGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
genomic: TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCATgtaagtgttg ... atatatgtagGGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
EST: gi|76012499|gb|DT939669.1|DT939669
EST:     TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCAT                         GGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
genomic: TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCATgtaagtgttg ... atatatgtagGGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
EST: gi|50333900|gb|CO529026.1|CO529026
EST:     TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCAT                         GGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
genomic: TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCATgtaagtgttg ... atatatgtagGGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
EST: gi|30088407|gb|CB886612.1|CB886612
EST:     TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCAT                         GGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
genomic: TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCATgtaagtgttg ... atatatgtagGGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
EST: gi|76015258|gb|DT942428.1|DT942428
EST:     TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCAT                         GGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
genomic: TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCATgtaagtgttg ... atatatgtagGGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
EST: gi|211338108|gb|FL126021.1|FL126021
EST:     TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCAT                         GGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
genomic: TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCATgtaagtgttg ... atatatgtagGGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
EST: gi|78108019|gb|DV526437.1|DV526437
EST:     TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCAT                         GGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
genomic: TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCATgtaagtgttg ... atatatgtagGGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
EST: gi|116816005|gb|EC858705.1|EC858705
EST:     TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCAT                         GGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATCCAGGCCATAAAGTT
genomic: TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCATgtaagtgttg ... atatatgtagGGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
EST: gi|31359967|gb|CD444324.1|CD444324
EST:     TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCAT                         GGCTCCTTGTCAGGAAATGGTTACGAGATGAAACATTCAGGCCATAAAGTT
genomic: TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCATgtaagtgttg ... atatatgtagGGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
EST: gi|211340497|gb|FL126026.1|FL126026
EST:     TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCAT                         GGCTCCTTGTCAGGAAATGGTTACGAGATGAAACATTCAGGCCATAAAGTT
genomic: TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCATgtaagtgttg ... atatatgtagGGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
EST: gi|211338109|gb|FL126022.1|FL126022
EST:     TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCAT                         GGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
genomic: TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCATgtaagtgttg ... atatatgtagGGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
EST: gi|91057234|gb|EB167652.1|EB167652
EST:     TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCAT                         GGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
genomic: TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCATgtaagtgttg ... atatatgtagGGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
EST: gi|74233446|gb|DT641360.1|DT641360
EST:     TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCAT                         GGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT
genomic: TACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCATgtaagtgttg ... atatatgtagGGCTCCTTGTCAGGAAATGGTTATGAGATGAAACATTCAGGCCATAAAGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAATGTTGTTTGGAGCTCAGTGACACCATCTTGTAATGCCTGTGATTTTACGGGAAATGGAGGATCATTCTGTCCATCCCATGTCTAAGTCTAACCATgtaagtgttggtatttatgctgtcaagaccttaaaccctaaacctgtgtctgtttgccataccacagatagttagctcattagctagcctatatatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT