Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgttctgttctttatgagttatgcgatccccgtggcatgttataactgctaggggttacatattgcttacctgctattgttgtgcggtttctgccgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCTCCTGAACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGT

Basic information

species Zea mays
transcript GRMZM2G041181_T01
intron # 2
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|76929603|gb|DV172080.1|DV172080
EST:     GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT                         AACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
genomic: GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
EST: gi|88755248|gb|DY539389.1|DY539389
EST:     GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT                         AACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
genomic: GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
EST: gi|211170206|gb|FL095741.1|FL095741
EST:     GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT                         AACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
genomic: GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
EST: gi|71301449|gb|DR786760.1|DR786760
EST:     GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT                         AACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
genomic: GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
EST: gi|211171878|gb|FL095747.1|FL095747
EST:     GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT                         AACACCAGAAACATGCCTCCTGCATCCAATTCTCGCCTTTCGCCGCTTCCT
genomic: GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
EST: gi|76018527|gb|DT945697.1|DT945697
EST:     GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT                         AACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
genomic: GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
EST: gi|22819595|gb|BU499685.1|BU499685
EST:     CAAGGCTGGCGGGCAGTCCAACTTCGAGCGGAGG-GCGTTTTACATGCCT                         AACACCAGAAACATGCCTCCTGCATCCAATTCGCGTCTTTCGCCGCTTCCT
genomic: CAAGGCTGGCGGGCAGTCCAACTTCG-GCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
EST: gi|211170205|gb|FL095740.1|FL095740
EST:     GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT                         AACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
genomic: GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
EST: gi|28566548|gb|CB278196.1|CB278196
EST:     GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT                         AACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
genomic: GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
EST: gi|74239804|gb|DT647718.1|DT647718
EST:     GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT                         AACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
genomic: GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
EST: gi|211171877|gb|FL095746.1|FL095746
EST:     GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT                         AACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
genomic: GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
EST: gi|211170209|gb|FL095744.1|FL095744
EST:     GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT                         AACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
genomic: GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
EST: gi|42491841|gb|CK700887.1|CK700887
EST:     GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT                         AACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
genomic: GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
EST: gi|149076171|gb|EE164763.2|EE164763
EST:     GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT                         AACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
genomic: GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
EST: gi|50322749|gb|CO517875.1|CO517875
EST:     GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT                         AACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
genomic: GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
EST: gi|37622034|gb|CF675087.1|CF675087
EST:     GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT                         AACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
genomic: GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
EST: gi|211170207|gb|FL095742.1|FL095742
EST:     GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT                         AACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
genomic: GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
EST: gi|211170208|gb|FL095743.1|FL095743
EST:     GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT                         AACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
genomic: GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
EST: gi|94472178|gb|EB701136.1|EB701136
EST:     GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT                         AACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
genomic: GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
EST: gi|211170204|gb|FL095739.1|FL095739
EST:     AAGGTCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATNGCCT                         AACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCC
genomic: AAGG-CTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACAT-GCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCC
EST: gi|38568932|gb|CF974817.1|CF974817
EST:     GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT                         AACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
genomic: GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
EST: gi|50325032|gb|CO520158.1|CO520158
EST:     GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT                         AACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
genomic: GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
EST: gi|211171876|gb|FL095745.1|FL095745
EST:     GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT                         AACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
genomic: GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
EST: gi|37361385|gb|CF602674.1|CF602674
EST:     GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCT                         AACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT
genomic: GCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 223

GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCTCCTGAACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 166

GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCTCCTGAACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 169

GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCTCCTGAACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 201

GAACAAGCGCGCGGCAAGGCTGGCGGGCAGTCCAACTTCGGCGGTGGTGCGTTTTACATGCCTgtgagttgtt ... cgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCTCCTGAACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggggttacatattgcttacctgctattgttgtgcggtttctgccgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCTCCTGAACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGT
              tgcttac  putative branch site (score: 201)
                                      tttctgcc  putative PPT
      ttacatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttgttctgttctttatgagttatgcgatccccgtggcatgttataactgctaggggttacatattgcttacctgctattgttgtgcggtttctgccgaaatgtagAACACCAGAAACATGCCTCCTGCATCCAATTCGCGCCTTTCGCCGCTTCCTCCTGAACCAGCAGACTTCAGTGCTACAGTGGACATACCCCTGGACTCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA