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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagcacgccactgctcactagactttttggtggcgcgcctttgccgcatttttcattaatataaggagaatcttgtttttttggggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAG

Basic information

species Zea mays
transcript GRMZM2G143602_T01
intron # 7
splice site 3'
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|61117728|gb|DN558689.1|DN558689
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG                         GCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacg ... ggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
EST: gi|33103216|gb|CF063176.1|CF063176
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG                         GCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacg ... ggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
EST: gi|60396112|gb|DN228981.1|DN228981
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG                         GCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacg ... ggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
EST: gi|4680837|gb|AI629507.1|AI629507
EST:     GTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG                         GCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
genomic: GTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacg ... ggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
EST: gi|71770652|gb|DR968589.1|DR968589
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG                         GCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacg ... ggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
EST: gi|16377160|gb|BI991802.1|BI991802
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG                         GCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacg ... ggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
EST: gi|60395786|gb|DN228656.1|DN228656
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG                         GCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacg ... ggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
EST: gi|60343609|gb|DN210582.1|DN210582
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG                         GCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacg ... ggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
EST: gi|21389960|gb|BQ528009.1|BQ528009
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG                         GCATAGCAGGAAACCC
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacg ... ggggatgcagGCATAGCAGGAAACCC
EST: gi|29576767|gb|CB616879.1|CB616879
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG                         GCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacg ... ggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
EST: gi|20507674|gb|BQ279724.1|BQ279724
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG                         GCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGAT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacg ... ggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGAT
EST: gi|60340369|gb|DN207342.1|DN207342
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG                         GCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacg ... ggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
EST: gi|211466861|gb|FL187159.1|FL187159
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG                         GCATAGCAGGAAACCCCTGGT-AAAGTTTATGAACGCAGATAACCAGCACC
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacg ... ggggatgcagGCATAGCAGGAAACCC-TGGTTAAAGTTTATGAACGCAGATAACCAGCACC
EST: gi|78073838|gb|DV502272.1|DV502272
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG                         GCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacg ... ggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
EST: gi|60395745|gb|DN228615.1|DN228615
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG                         GCATAGCAGGAAACCCTGGTTAAAGTTTATGAATGCAGATAACCAGCACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacg ... ggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
EST: gi|16379175|gb|BI992806.1|BI992806
EST:     ACCAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG                         GCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacg ... ggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgccgcatttttcattaatataaggagaatcttgtttttttggggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAG
              cattaat  putative branch site (score: 3)
        atttttcattaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagcacgccactgctcactagactttttggtggcgcgcctttgccgcatttttcattaatataaggagaatcttgtttttttggggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT