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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCTAGTGTGCTGTCAGCACTTGCTTTGGCATTCAACACAAATCTGTTCGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAGgtaatgttttttctctctccctggaaattctggttgtttttttacctcaagtagttaaccctgccaactaaattttttggtttccttcacaagggatctg...

Basic information

species Zea mays
transcript GRMZM2G040933_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G040933_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os09g29430.1 (Oryza sativa), 5'ss of exon 3
GTTCCTAGTGTGCTGTCAGCACTTGCTTTGGCATTCAACACAAATCTGTTCGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAGgtaa-tgttttttctctctccctggaaattctggttgtttttttacct-caagtagttaaccctgccaactaaattttttggtttccttcacaagggatctg
|||||| | ||||||||||| ||||||||||||||||||||||||||||| |||||| | |||||||||||||| || ||||||||||| ||||| |||||||| |   | ||||   |  |||||  |  |     | |||| |  | |||   | | |||||   ||  ||       ||   |    ||||        
GTTCCTCGAGTGCTGTCAGCTCTTGCTTTGGCATTCAACACAAATCTGTTTGGTGCACTAACTCATTATAGTAGCGGACAGGCTGCAGTGTACTTTGGAGgtaaattcatgttctacttttctggatttcatttcattattttcatttacaaacgggttaccctaaaaaaaaagagcagaggaagcaaaaacaacatgct--
















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|71774471|gb|DR972349.1|DR972349
EST:     CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAG                         CCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
genomic: CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAGgtaatgtttt ... tgttgtgcagCCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
EST: gi|32920982|gb|CF025794.1|CF025794
EST:     CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAG                         CCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
genomic: CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAGgtaatgtttt ... tgttgtgcagCCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
EST: gi|32920645|gb|CF025457.1|CF025457
EST:     CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAG                         CCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
genomic: CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAGgtaatgtttt ... tgttgtgcagCCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
EST: gi|211318200|gb|FL216607.1|FL216607
EST:     CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAG                         CCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
genomic: CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAGgtaatgtttt ... tgttgtgcagCCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
EST: gi|76021275|gb|DT948445.1|DT948445
EST:     CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAG                         CCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
genomic: CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAGgtaatgtttt ... tgttgtgcagCCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
EST: gi|32921667|gb|CF026479.1|CF026479
EST:     CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAG                         CCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
genomic: CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAGgtaatgtttt ... tgttgtgcagCCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
EST: gi|33096299|gb|CF056293.1|CF056293
EST:     CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAG                         CCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
genomic: CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAGgtaatgtttt ... tgttgtgcagCCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
EST: gi|32921119|gb|CF025931.1|CF025931
EST:     CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAG                         CCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
genomic: CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAGgtaatgtttt ... tgttgtgcagCCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
EST: gi|78121143|gb|DV539527.1|DV539527
EST:     CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAG                         CCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
genomic: CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAGgtaatgtttt ... tgttgtgcagCCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
EST: gi|110954131|gb|EE174183.1|EE174183
EST:     CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAG                         CCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
genomic: CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAGgtaatgtttt ... tgttgtgcagCCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
EST: gi|78092282|gb|DV520656.1|DV520656
EST:     CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAG                         CCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
genomic: CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAGgtaatgtttt ... tgttgtgcagCCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
EST: gi|71299453|gb|DR785734.1|DR785734
EST:     CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTTGGAG                         CCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
genomic: CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAGgtaatgtttt ... tgttgtgcagCCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
EST: gi|116829124|gb|EC864545.1|EC864545
EST:     CGGTGCAATCACTCATTATAGTAGTGGGCAAGCTGCAGTATACTTCGGAA                         CCCGGTATATGGAGCTTCCCGATGTTTTCAGGCTGG
genomic: CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAGgtaatgtttt ... tgttgtgcagCCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGG
EST: gi|78124302|gb|DV542686.1|DV542686
EST:     CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAG                         CCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
genomic: CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAGgtaatgtttt ... tgttgtgcagCCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
EST: gi|78092093|gb|DV520467.1|DV520467
EST:     CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAG                         CCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT
genomic: CGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAGgtaatgtttt ... tgttgtgcagCCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCT

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: 47 (upstream exon), 49 (downstream exon)
Score: 31

GTTCCTAGTGTGCTGTCAGCACTTGCTTTGGCATTCAACACAAATCTGTTCGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAGgtaatgtttt ... tgttgtgcagCCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCTTGGCTAACACGTTAATCTGGGGAGTTGTTGGAACCATCTGGTGGAAATT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 102

GTTCCTAGTGTGCTGTCAGCACTTGCTTTGGCATTCAACACAAATCTGTTCGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAGgtaatgtttt ... tgttgtgcagCCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCTTGGCTAACACGTTAATCTGGGGAGTTGTTGGAACCATCTGGTGGAAATT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 25

GTTCCTAGTGTGCTGTCAGCACTTGCTTTGGCATTCAACACAAATCTGTTCGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAGgtaatgtttt ... tgttgtgcagCCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCTTGGCTAACACGTTAATCTGGGGAGTTGTTGGAACCATCTGGTGGAAATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 66

GTTCCTAGTGTGCTGTCAGCACTTGCTTTGGCATTCAACACAAATCTGTTCGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAGgtaatgtttt ... tgttgtgcagCCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCTTGGCTAACACGTTAATCTGGGGAGTTGTTGGAACCATCTGGTGGAAATT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCCTAGTGTGCTGTCAGCACTTGCTTTGGCATTCAACACAAATCTGTTCGGTGCAATCACTCATTATAGTAGTGGGCAGGCTGCAGTATACTTCGGAGgtaatgttttttctctctccctggaaattctggttgtttttttacctcaagtagttaaccctgccaactaaattttttggtttccttcacaagggatctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG