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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgttgaactatcatcagcaaaaggctctgatgcccctgatattatttatgcagtcatttccaacaatagctaattaatatgctttttatcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG

Basic information

species Zea mays
transcript GRMZM2G086805_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|7844125|gb|AW787328.1|AW787328
EST:     GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGG                         AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
genomic: GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
EST: gi|29129751|gb|CB380455.1|CB380455
EST:     AACTTCACTGG                         AATTATCTCTCTGATGGACCCCAGTAGGAG-NGGGCAGCCCGTTGGTTGAG
genomic: AACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
EST: gi|32930934|gb|CF035746.1|CF035746
EST:     CACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGG                         AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
genomic: CACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
EST: gi|211373132|gb|FL346967.1|FL346967
EST:     GACAGAGAGCACGACAACGTSSTCAACTGCACCACCCCCAACTTCACTGG                         AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
genomic: GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
EST: gi|28986940|gb|CB351384.1|CB351384
EST:     CCAACTTCACTGG                         AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
genomic: CCAACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
EST: gi|211388869|gb|FL452911.1|FL452911
EST:     GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGG                         AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
genomic: GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
EST: gi|37378989|gb|CF626218.1|CF626218
EST:     GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGG                         AATTATCTCTCTGATGGACCCCAGTTGGAGCTGGGCAGCCCGTTGGTTGAG
genomic: GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
EST: gi|4730597|gb|AI649763.1|AI649763
EST:     GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGG                         AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
genomic: GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
EST: gi|32943412|gb|CF048231.1|CF048231
EST:     GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGG                         AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
genomic: GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
EST: gi|37375940|gb|CF624458.1|CF624458
EST:     GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGG                         AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
genomic: GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
EST: gi|91869839|gb|EB400567.1|EB400567
EST:     GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGG                         AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
genomic: GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
EST: gi|45847108|gb|CN071051.1|CN071051
EST:     ACAGAGAGCACGACAACGTCGTCGAACTGCACCACCCCCAACTTCACTGG                         AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
genomic: ACAGAGAGCACGACAACGTCGTC-AACTGCACCACCCCCAACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
EST: gi|30087685|gb|CB885891.1|CB885891
EST:     TGCACCACCCCCAACTTCACTGG                         AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
genomic: TGCACCACCCCCAACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
EST: gi|93015254|gb|EB640774.1|EB640774
EST:     GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGG                         AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
genomic: GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
EST: gi|60339603|gb|DN206576.1|DN206576
EST:     GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGG                         AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
genomic: GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
EST: gi|211528033|gb|FL311002.1|FL311002
EST:     GACAGAGAGCACGACAACGTSSTCAACTGCACCACCCCCAACTTCACTGG                         AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
genomic: GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
EST: gi|60398153|gb|DN230969.1|DN230969
EST:     GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGG                         AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
genomic: GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
EST: gi|211342808|gb|FL351909.1|FL351909
EST:     GACAGAGAGCACGACAACGTSK-CAACTGCACCACCCCCAACTTCACTGG                         AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
genomic: GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
EST: gi|60351934|gb|DN218907.1|DN218907
EST:     GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGG                         AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
genomic: GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
EST: gi|32857871|gb|CD997552.1|CD997552
EST:     GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGG                         AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
genomic: GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
EST: gi|7844126|gb|AW787329.1|AW787329
EST:     GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGG                         AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG
genomic: GACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAG

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: 398

TTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 306

TTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 325

TTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG


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

TTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGGgtaactccac ... tcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttatgcagtcatttccaacaatagctaattaatatgctttttatcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG
                            aattaat  putative branch site (score: 201)
                                      ctttttatctt  putative PPT
                           taattaatatgctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgttgaactatcatcagcaaaaggctctgatgcccctgatattatttatgcagtcatttccaacaatagctaattaatatgctttttatcttgtgcagAATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT