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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttttcattctactcgtgattccagatccttttatgtgcttaactcgtactcaaacacaggattttgaatatgtgaacttctgcatgaaacctttataggctccatgccttgagttgatatggcaatttattggccgtatcctaggccctggaagctgaccaccttttcccccctccagGCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAAGGTGGAATTCGGGCTACCTGACTTGGAGGGCCGTACCCAAATTTTCAAG

Basic information

species Zea mays
transcript GRMZM2G110185_T03
intron # 8
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|30032173|gb|CB834024.1|CB834024
EST:     GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAG                         GCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
genomic: GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAGgtattttttc ... ccccctccagGCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
EST: gi|60342770|gb|DN209743.1|DN209743
EST:     GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAG                         GCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
genomic: GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAGgtattttttc ... ccccctccagGCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
EST: gi|78085798|gb|DV514191.1|DV514191
EST:     GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAG                         GCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
genomic: GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAGgtattttttc ... ccccctccagGCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
EST: gi|32940894|gb|CF045713.1|CF045713
EST:     GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAG                         GCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
genomic: GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAGgtattttttc ... ccccctccagGCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
EST: gi|60350973|gb|DN217946.1|DN217946
EST:     GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAG                         GCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
genomic: GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAGgtattttttc ... ccccctccagGCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
EST: gi|12973054|gb|BG268289.1|BG268289
EST:     ATCAAAGTTCTCATGGCCACTAATAG                         GCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
genomic: ATCAAAGTTCTCATGGCCACTAATAGgtattttttc ... ccccctccagGCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
EST: gi|29129891|gb|CB380595.1|CB380595
EST:     GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAG                         GCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
genomic: GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAGgtattttttc ... ccccctccagGCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
EST: gi|1298504|gb|W21754.1|W21754
EST:     AAAGTTCTCATGGCCACTAATAG                         GCCTGATACCTTGGATCCTGCACTTCTGCNCCCTGGTCGCTTGGACAGAAA
genomic: AAAGTTCTCATGGCCACTAATAGgtattttttc ... ccccctccagGCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
EST: gi|60344174|gb|DN211147.1|DN211147
EST:     GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAG                         GCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
genomic: GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAGgtattttttc ... ccccctccagGCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
EST: gi|33104358|gb|CF064318.1|CF064318
EST:     GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAG                         GCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
genomic: GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAGgtattttttc ... ccccctccagGCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
EST: gi|211078711|gb|FL469455.1|FL469455
EST:     GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAG                         GCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
genomic: GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAGgtattttttc ... ccccctccagGCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
EST: gi|60398345|gb|DN231161.1|DN231161
EST:     GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAG                         GCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
genomic: GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAGgtattttttc ... ccccctccagGCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
EST: gi|1298502|gb|W21752.1|W21752
EST:     GAGGGAACATCAAAGTTCTCATGGCCACTAATAG                         GCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
genomic: GAGGGAACATCAAAGTTCTCATGGCCACTAATAGgtattttttc ... ccccctccagGCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
EST: gi|12968378|gb|BG265324.1|BG265324
EST:     GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAG                         GCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
genomic: GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAGgtattttttc ... ccccctccagGCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
EST: gi|211007573|gb|FL233622.1|FL233622
EST:     GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAG                         GCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
genomic: GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAGgtattttttc ... ccccctccagGCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
EST: gi|32849113|gb|CD988794.1|CD988794
EST:     GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAG                         GCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
genomic: GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAGgtattttttc ... ccccctccagGCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
EST: gi|60397964|gb|DN230780.1|DN230780
EST:     GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAG                         GCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
genomic: GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAGgtattttttc ... ccccctccagGCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
EST: gi|37376995|gb|CF625066.1|CF625066
EST:     GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAG                         GCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA
genomic: GATGGGTTTGATGCAAGAGGGAACATCAAAGTTCTCATGGCCACTAATAGgtattttttc ... ccccctccagGCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttattggccgtatcctaggccctggaagctgaccaccttttcccccctccagGCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAAGGTGGAATTCGGGCTACCTGACTTGGAGGGCCGTACCCAAATTTTCAAG
                             agctgac  putative branch site (score: 3)
                               ctgaccaccttttccc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttttcattctactcgtgattccagatccttttatgtgcttaactcgtactcaaacacaggattttgaatatgtgaacttctgcatgaaacctttataggctccatgccttgagttgatatggcaatttattggccgtatcctaggccctggaagctgaccaccttttcccccctccagGCCTGATACCTTGGATCCTGCACTTCTGCGCCCTGGTCGCTTGGACAGAAAGGTGGAATTCGGGCTACCTGACTTGGAGGGCCGTACCCAAATTTTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG