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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgcaactgctgctaatactccttcggtttacactcaatagtttatttgatatactgccttataaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCTTCGTGGACTGAATAGTGAATTTTGTCCAGCTTAGTGTGGAGATGGTGAG

Basic information

species Zea mays
transcript GRMZM2G015238_T01
intron # 11
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|67016782|gb|CO445531.1|CO445531
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|60344383|gb|DN211356.1|DN211356
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|5597321|gb|AI891419.1|AI891419
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|60356904|gb|DN223877.1|DN223877
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|18963876|gb|BM660679.1|BM660679
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|5791196|gb|AI977988.1|AI977988
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|44900754|gb|CK827299.1|CK827299
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|78022596|gb|DV490983.1|DV490983
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|21626121|gb|BQ621042.1|BQ621042
EST:     GCATTGATCGGAAGTCAGGGCGTGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|37399452|gb|CF637054.1|CF637054
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|88758529|gb|DY542898.1|DY542898
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|71442594|gb|DR823644.1|DR823644
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|78544674|gb|DV622172.1|DV622172
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|6527073|gb|AW216288.1|AW216288
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|37393818|gb|CF634175.1|CF634175
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|24763832|gb|CA399003.1|CA399003
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|89249905|gb|DY621691.1|DY621691
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|6056928|gb|AW091333.1|AW091333
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|60398821|gb|DN231637.1|DN231637
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|76280769|gb|DV020337.1|DV020337
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|5713974|gb|AI943959.1|AI943959
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|17931189|gb|BM268149.1|BM268149
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|67032589|gb|CO461338.1|CO461338
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|211501366|gb|FL476265.1|FL476265
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|9953312|gb|BE639895.1|BE639895
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|32934871|gb|CF039683.1|CF039683
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
EST: gi|71450194|gb|DR831244.1|DR831244
EST:     GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATG                         ATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT
genomic: GCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCT

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), 48 (downstream exon)
Score: 146

CCTGTGTACCAGCACTGAGGACAGTCCGCAGACGAATCCAATAATTGGTCGCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCTTCGTGGACTGAATAGTGAATTTTGTCCAGCTTAGTGTGGAGATGGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 265

CCTGTGTACCAGCACTGAGGACAGTCCGCAGACGAATCCAATAATTGGTCGCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCTTCGTGGACTGAATAGTGAATTTTGTCCAGCTTAGTGTGGAGATGGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

CCTGTGTACCAGCACTGAGGACAGTCCGCAGACGAATCCAATAATTGGTCGCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCTTCGTGGACTGAATAGTGAATTTTGTCCAGCTTAGTGTGGAGATGGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 170

CCTGTGTACCAGCACTGAGGACAGTCCGCAGACGAATCCAATAATTGGTCGCATTGATCGGAAGTCAGGGCATGGAGCTGGCAGGCCAACTCAAAAAATGgtttgtgcaa ... taaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCTTCGTGGACTGAATAGTGAATTTTGTCCAGCTTAGTGTGGAGATGGTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actccttcggtttacactcaatagtttatttgatatactgccttataaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCTTCGTGGACTGAATAGTGAATTTTGTCCAGCTTAGTGTGGAGATGGTGAG
                           atttgat  putative branch site (score: 170)
                   aatagtttatttgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgcaactgctgctaatactccttcggtttacactcaatagtttatttgatatactgccttataaatttcagATTGACGAAGCTGCAGACAGATATAGCTTTATGGCAAAAATGTTAGGGGCTTCGTGGACTGAATAGTGAATTTTGTCCAGCTTAGTGTGGAGATGGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG