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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAAATTTAATCGGTGGACCTCGCCTTATCTCGACAAAGATGCTGAGGCAGTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGATgtaattacctcactgaattgaaattagtggccacctgtgttttgtttctgtacatgggaattgtgactttttttggtttccaactgcag

Basic information

species Zea mays
transcript GRMZM2G464137_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G464137_T03 (Zea mays), 5'ss of exon 3
lower sequence: Vv03s0091g00080.t01 (Vitis vinifera), 5'ss of exon 3
CCAAATTTAATCGGTGGACCTCGCCTTATCTCGACAAAGATGCTGAGGCAGTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGATgtaat-------------tacctcactg--------aattgaaattagtg--gccacctgtgttttgtttctgtacatgggaattgtgactttttttggtttccaactgcag------------
|  | |  ||||||||||| || |||||||| |||   ||||||||||||||||| |||||| |     | ||| | ||||| || | | ||||||| ||||| |             ||||||| |         |||  ||| || |      |   |   |||  ||||| |      |  |   | |  |||   |  | |  |  |             
CTCAGTACAATCGGTGGACTTCTCCTTATCTTGACCGTGATGCTGAGGCAGTTCGAGAGGATAACATTTTGAAGCTTGAAGTTGCCGAGTTGAAATCTATgtagtgcttccatatcagtacctcatttctttacgtaatataaaatatttctattaatagcagtttaattctgaagtaaacaggttgaaatcctttctatgcctagttagaatctattttgcag
















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|76925788|gb|DV170594.1|DV170594
EST:     TTCGCGAGGATGATGAGCTNCA-GTTGGAAGTAGCTGGGCTGAAATCGAT                         GTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTC
genomic: TTCGCGAGGATGATGAGCT-CAAGTTGGAAGTAGCTGGGCTGAAATCGATgtaattacct ... ccaactgcagGTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTC
EST: gi|148931973|gb|EC875233.2|EC875233
EST:     GTTCGCGAGGATGATGAGCTCAAGTTGGGAGTAGCTGGGCTGAAATCGAT                         GTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTC
genomic: GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGATgtaattacct ... ccaactgcagGTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTC
EST: gi|148962543|gb|EE013418.2|EE013418
EST:     GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGAT                         GTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTC
genomic: GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGATgtaattacct ... ccaactgcagGTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTC
EST: gi|71432514|gb|DR813564.1|DR813564
EST:     GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGAT                         GTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTC
genomic: GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGATgtaattacct ... ccaactgcagGTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTC
EST: gi|148969592|gb|EE020430.2|EE020430
EST:     GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGAT                         GTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCTACACTGGTTC
genomic: GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGATgtaattacct ... ccaactgcagGTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTC
EST: gi|32929857|gb|CF034669.1|CF034669
EST:     GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGAT                         GTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTC
genomic: GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGATgtaattacct ... ccaactgcagGTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTC
EST: gi|76913361|gb|DV165093.1|DV165093
EST:     GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGAT                         GTTTATCGAGAGAGCTCAAGCTCTGA
genomic: GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGATgtaattacct ... ccaactgcagGTTTATCGAGAGAGCTCAAGCTCTGA
EST: gi|76292759|gb|DV032327.1|DV032327
EST:     GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGAT                         GTTTATCGAGAGAGCTNCA-GCTCTGATTCATGGAGATCTCCACACTGGTT
genomic: GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGATgtaattacct ... ccaactgcagGTTTATCGAGAGAGCT-CAAGCTCTGATTCATGGAGATCTCCACACTGGTT
EST: gi|78114422|gb|DV532811.1|DV532811
EST:     GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGAT                         GTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCCCACTGGTTC
genomic: GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGATgtaattacct ... ccaactgcagGTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTC
EST: gi|149048896|gb|EE048395.2|EE048395
EST:     GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGAT                         GTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTC
genomic: GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGATgtaattacct ... ccaactgcagGTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTC
EST: gi|32929601|gb|CF034413.1|CF034413
EST:     GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGAT                         GTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTC
genomic: GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGATgtaattacct ... ccaactgcagGTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTC
EST: gi|32928909|gb|CF033721.1|CF033721
EST:     GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGAT                         GTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTC
genomic: GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGATgtaattacct ... ccaactgcagGTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTC
EST: gi|148938568|gb|EC882889.2|EC882889
EST:     GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGAT                         GTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGGTC
genomic: GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGATgtaattacct ... ccaactgcagGTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTC
EST: gi|149080185|gb|EE169203.2|EE169203
EST:     GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGAT                         GTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTC
genomic: GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGATgtaattacct ... ccaactgcagGTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTC
EST: gi|149100125|gb|EE186180.2|EE186180
EST:     GTTCGCGAGGATGATGAGCTCANGTTGGAAGTAGCTGGGCTGAAATCGAT                         GTTTATCGAGAGAGC
genomic: GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGATgtaattacct ... ccaactgcagGTTTATCGAGAGAGC
EST: gi|71430317|gb|DR811367.1|DR811367
EST:     GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGAT                         GTTTATCGAGAGAG
genomic: GTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGATgtaattacct ... ccaactgcagGTTTATCGAGAGAG

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: 110

CCAAATTTAATCGGTGGACCTCGCCTTATCTCGACAAAGATGCTGAGGCAGTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGATgtaattacct ... ccaactgcagGTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTCTATCATGGTGACCGAAGGTTCAACTCAAGTCATTGATCCAGAATTTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 304

CCAAATTTAATCGGTGGACCTCGCCTTATCTCGACAAAGATGCTGAGGCAGTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGATgtaattacct ... ccaactgcagGTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTCTATCATGGTGACCGAAGGTTCAACTCAAGTCATTGATCCAGAATTTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 283

CCAAATTTAATCGGTGGACCTCGCCTTATCTCGACAAAGATGCTGAGGCAGTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGATgtaattacct ... ccaactgcagGTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTCTATCATGGTGACCGAAGGTTCAACTCAAGTCATTGATCCAGAATTTGGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 63

CCAAATTTAATCGGTGGACCTCGCCTTATCTCGACAAAGATGCTGAGGCAGTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGATgtaattacct ... ccaactgcagGTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTCTATCATGGTGACCGAAGGTTCAACTCAAGTCATTGATCCAGAATTTGGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAAATTTAATCGGTGGACCTCGCCTTATCTCGACAAAGATGCTGAGGCAGTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGATgtaattacctcactgaattgaaattagtggccacctgtgttttgtttctgtacatgggaattgtgactttttttggtttccaactgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG