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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgtgtgtgtgtgtgtgggggggggggggggactgcattttgcaggttgcggtacttacccggtccatcggttgcttgatttggtttcttattatgcagCGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCTCAAGATTTTTTCTGTGTTCTTTAGAGAGCAGCCATGGACGAGTGGATTC

Basic information

species Zea mays
transcript GRMZM2G091503_T04
intron # 1
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|211515522|gb|FL138438.1|FL138438
EST:     CCATCGGGGACGAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGAC                         CGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
genomic: CCATCGGGGACGAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGACgtagccctcc ... tattatgcagCGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
EST: gi|211513176|gb|FL138432.1|FL138432
EST:     CCATCGGGGACGAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGAC                         CGGTCGAGGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTC
genomic: CCATCGGGGACGAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGACgtagccctcc ... tattatgcagCGGTCGA-GCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTC
EST: gi|40333811|gb|CK367881.1|CK367881
EST:     GGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGAC                         CGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
genomic: GGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGACgtagccctcc ... tattatgcagCGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
EST: gi|211515518|gb|FL138434.1|FL138434
EST:     TTCTGCCGCGCGGCGAC                         CGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
genomic: TTCTGCCGCGCGGCGACgtagccctcc ... tattatgcagCGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
EST: gi|26557413|gb|CA829648.1|CA829648
EST:     GATACTTCTGCCGCGCGGCGA-                         CGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
genomic: GATACTTCTGCCGCGCGGCGACgtagccctcc ... tattatgcagCGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
EST: gi|60339827|gb|DN206800.1|DN206800
EST:     AGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGAC                         CGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
genomic: AGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGACgtagccctcc ... tattatgcagCGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
EST: gi|211513168|gb|FL138424.1|FL138424
EST:     ATCGGGGACGAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGAC                         CGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
genomic: ATCGGGGACGAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGACgtagccctcc ... tattatgcagCGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
EST: gi|211513170|gb|FL138426.1|FL138426
EST:     CCATCGGGGACGAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGAC                         CGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
genomic: CCATCGGGGACGAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGACgtagccctcc ... tattatgcagCGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
EST: gi|37375548|gb|CF624218.1|CF624218
EST:     GGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGAC                         CGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
genomic: GGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGACgtagccctcc ... tattatgcagCGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
EST: gi|26456106|gb|CA827689.1|CA827689
EST:     ATACTTCTGCCGCGCGG-GAC                         CGG-CGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
genomic: ATACTTCTGCCGCGCGGCGACgtagccctcc ... tattatgcagCGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
EST: gi|211515523|gb|FL138439.1|FL138439
EST:     CCATCGGGGACGAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGAC                         CGGTCGAGCAAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
genomic: CCATCGGGGACGAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGACgtagccctcc ... tattatgcagCGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
EST: gi|211515520|gb|FL138436.1|FL138436
EST:     ATCGGGGACGAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGAC                         CGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
genomic: ATCGGGGACGAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGACgtagccctcc ... tattatgcagCGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
EST: gi|89106845|gb|DY577062.1|DY577062
EST:     CCATCGGGGACGAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGAC                         CGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
genomic: CCATCGGGGACGAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGACgtagccctcc ... tattatgcagCGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
EST: gi|22935960|gb|BU572235.1|BU572235
EST:     GGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGAC                         CGGTCGAGCGAAATCGATCTACCCCAGG-GCGGCGGGCGCGGCTTTATTCT
genomic: GGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGACgtagccctcc ... tattatgcagCGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
EST: gi|211513175|gb|FL138431.1|FL138431
EST:     ATCGGGGACGAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGAC                         CGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
genomic: ATCGGGGACGAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGACgtagccctcc ... tattatgcagCGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
EST: gi|211515531|gb|FL138440.1|FL138440
EST:     ATCGGGGACGAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGAC                         CGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
genomic: ATCGGGGACGAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGACgtagccctcc ... tattatgcagCGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
EST: gi|22818765|gb|BU498855.1|BU498855
EST:     GCCGCGCGGCGA-                         CGGTCGAGCG-AATCGATCTACCCCAGG-GCGGCGGGCGCGGCTTTATTCT
genomic: GCCGCGCGGCGACgtagccctcc ... tattatgcagCGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
EST: gi|26559708|gb|CA831943.1|CA831943
EST:     CCATCGGGGACTAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGAC                         CGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
genomic: CCATCGGGGACGAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGACgtagccctcc ... tattatgcagCGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
EST: gi|211513172|gb|FL138428.1|FL138428
EST:     ATCGGGGACGAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGAC                         CGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
genomic: ATCGGGGACGAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGACgtagccctcc ... tattatgcagCGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
EST: gi|32914426|gb|CF019238.1|CF019238
EST:     CCATCGGGGACCAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGAC                         CGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
genomic: CCATCGGGGACGAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGACgtagccctcc ... tattatgcagCGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
EST: gi|211515519|gb|FL138435.1|FL138435
EST:     CCATCGGGGACGAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGA-                         CGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT
genomic: CCATCGGGGACGAGGGACTGGGAGCCAGGATACTTCTGCCGCGCGGCGACgtagccctcc ... tattatgcagCGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttgcggtacttacccggtccatcggttgcttgatttggtttcttattatgcagCGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCTCAAGATTTTTTCTGTGTTCTTTAGAGAGCAGCCATGGACGAGTGGATTC
                                        tttcttatt  CT-rich tract
                                        tttcttattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgtgtgtgtgtgtgtgggggggggggggggactgcattttgcaggttgcggtacttacccggtccatcggttgcttgatttggtttcttattatgcagCGGTCGAGCGAAATCGATCTACCCCAGGTGCGGCGGGCGCGGCTTTATTCTCAAGATTTTTTCTGTGTTCTTTAGAGAGCAGCCATGGACGAGTGGATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA