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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgcccccatctgcttcgcttgcgtcactctctccctccggctcagagttctctgctgactggtttccggctgtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG

Basic information

species Zea mays
transcript GRMZM2G153087_T01
intron # 1
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|211268211|gb|FL248427.1|FL248427
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211268210|gb|FL248426.1|FL248426
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211265771|gb|FL248408.1|FL248408
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|76292992|gb|DV032560.1|DV032560
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211268209|gb|FL248425.1|FL248425
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211265767|gb|FL248404.1|FL248404
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|71326250|gb|DR799818.1|DR799818
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211265779|gb|FL248416.1|FL248416
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|76282004|gb|DV021572.1|DV021572
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211268204|gb|FL248420.1|FL248420
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|71772104|gb|DR970041.1|DR970041
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|149014987|gb|EE044728.2|EE044728
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211265775|gb|FL248412.1|FL248412
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|37416887|gb|CF646095.1|CF646095
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211265773|gb|FL248410.1|FL248410
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211265772|gb|FL248409.1|FL248409
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|78075129|gb|DV503563.1|DV503563
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211265769|gb|FL248406.1|FL248406
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211268203|gb|FL248419.1|FL248419
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|76013927|gb|DT941097.1|DT941097
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211265778|gb|FL248415.1|FL248415
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211268206|gb|FL248422.1|FL248422
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211265780|gb|FL248417.1|FL248417
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|211265776|gb|FL248413.1|FL248413
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
EST: gi|71311486|gb|DR792098.1|DR792098
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCG                         ATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG

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: 46 (upstream exon), 48 (downstream exon)
Score: 116

GCCGGCTTTCCGGGCACGCAGCCGGTCTCCCGCTCGCCGGAGGACGTCTTCCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 180

GCCGGCTTTCCGGGCACGCAGCCGGTCTCCCGCTCGCCGGAGGACGTCTTCCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 282

GCCGGCTTTCCGGGCACGCAGCCGGTCTCCCGCTCGCCGGAGGACGTCTTCCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 50

GCCGGCTTTCCGGGCACGCAGCCGGTCTCCCGCTCGCCGGAGGACGTCTTCCGGGACTACCGCGCGCGCCAGGCCGGCCTGATCAGGGCGCTCACCACCGgtaatgcccc ... gtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctctccctccggctcagagttctctgctgactggtttccggctgtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG
                          tgctgac  putative branch site (score: 50)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgcccccatctgcttcgcttgcgtcactctctccctccggctcagagttctctgctgactggtttccggctgtcgctgcagATGTGGAGAAGTTCTACGTGATGTGCGACCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT