Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatattttgtgattttcttctatcacaccttaacgagtgcgttcccttaagttttctattgtgaaccaaaataacattatgttatttgatttcctccataatctgcaattttcttttaatggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC

Basic information

species Zea mays
transcript GRMZM2G097995_T02
intron # 3
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|6342791|gb|AW165615.1|AW165615
EST:     AGATCTCAACAGCCTCGAGAACCAAAGTTGAG                         TTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
genomic: AGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
EST: gi|6431871|gb|AW172075.1|AW172075
EST:     AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG                         TTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
genomic: AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
EST: gi|32165086|gb|CD670404.1|CD670404
EST:     AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG                         TTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
genomic: AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
EST: gi|211490460|gb|FL154418.1|FL154418
EST:     AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG                         TTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
genomic: AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
EST: gi|32825283|gb|CD965005.1|CD965005
EST:     GATCTCAACAGCCTCGAGAACCAAAGTTGAG                         CTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
genomic: GATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
EST: gi|28910854|gb|CB331648.1|CB331648
EST:     AGCAAAAAACGCCCCTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG                         TTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
genomic: AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
EST: gi|211525931|gb|FL453813.1|FL453813
EST:     AGCAAAAAACGCCACTYTAGATYTCAACAGCCTCGAGAACCAAAGTTGAG                         TTGGAACMCAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
genomic: AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
EST: gi|22472576|gb|BU037056.1|BU037056
EST:     AGCAAAAAACGCCCCTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG                         TTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
genomic: AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
EST: gi|26558641|gb|CA830876.1|CA830876
EST:     AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG                         TTGGAACACAACGTATGAAA
genomic: AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAA
EST: gi|29130525|gb|CB381229.1|CB381229
EST:     CCAAAGTTGAG                         TTGGAACCCAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
genomic: CCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
EST: gi|87156696|gb|DY401485.1|DY401485
EST:     AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG                         TTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
genomic: AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
EST: gi|31664502|gb|CD573435.1|CD573435
EST:     AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG                         TTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
genomic: AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
EST: gi|18171092|gb|BM340932.1|BM340932
EST:     AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG                         TTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
genomic: AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
EST: gi|29130220|gb|CB380924.1|CB380924
EST:     AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGCTGAG                         TTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAA
genomic: AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAA
EST: gi|87155503|gb|DY400292.1|DY400292
EST:     AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG                         TTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
genomic: AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
EST: gi|28909927|gb|CB331169.1|CB331169
EST:     AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG                         TTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
genomic: AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
EST: gi|31664503|gb|CD573436.1|CD573436
EST:     AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG                         TTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
genomic: AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
EST: gi|32792334|gb|CD944570.1|CD944570
EST:     GATCTCAACAGCCTCGAGAACCAAAGTTGAG                         TTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
genomic: GATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
EST: gi|32807750|gb|CD959984.1|CD959984
EST:     GATCTCAACAGCCTCGAGAACCAAAGTTGAG                         CTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
genomic: GATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
EST: gi|29543916|gb|CB604296.1|CB604296
EST:     AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG                         TTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
genomic: AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
EST: gi|211490455|gb|FL154413.1|FL154413
EST:     AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG                         CTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
genomic: AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
EST: gi|29543917|gb|CB604297.1|CB604297
EST:     AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG                         TTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
genomic: AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
EST: gi|31909751|gb|CD651076.1|CD651076
EST:     AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG                         TTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
genomic: AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
EST: gi|21987228|gb|BQ778756.1|BQ778756
EST:     AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGCTGAG                         TTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
genomic: AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
EST: gi|22472577|gb|BU037057.1|BU037057
EST:     AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG                         TTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
genomic: AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
EST: gi|29544694|gb|CB605074.1|CB605074
EST:     AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG                         TTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA
genomic: AGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCA

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: 49 (upstream exon), 49 (downstream exon)
Score: 141

GTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 120

GTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 138

GTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 97

GTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAGgtgaatattt ... tggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattatgttatttgatttcctccataatctgcaattttcttttaatggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC
                                       ttttaat  putative branch site (score: 97)
                                aattttcttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaatattttgtgattttcttctatcacaccttaacgagtgcgttcccttaagttttctattgtgaaccaaaataacattatgttatttgatttcctccataatctgcaattttcttttaatggtgtacagTTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA