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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAGTGCGCTCGTCGACTCCACTCAGCTCTCTCGCTCACTCTCCTCCCCCAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgcacgggtttcctattccccgccgccgcggcctctcgctcccctctctctgcgcggcctgctgactcccgtctccgcgttcgttctcccag

Basic information

species Zea mays
transcript GRMZM2G022777_T01
intron # 1
splice site 5'
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|148995361|gb|EE034575.2|EE034575
EST:     CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
genomic: CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|91876817|gb|EB406774.1|EB406774
EST:     CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
genomic: CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|211305002|gb|FL154237.1|FL154237
EST:     CAAGGCCCCAGAGACAGGCAGCCGGCGAGGCCCGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGGGGCAAGAAGGAACCCGAG
genomic: CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|148933119|gb|EC876754.2|EC876754
EST:     CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
genomic: CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|31355560|gb|CD439917.1|CD439917
EST:     CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAATCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
genomic: CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|76933170|gb|DV173349.1|DV173349
EST:     CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
genomic: CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|211305003|gb|FL154238.1|FL154238
EST:     CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
genomic: CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|211305001|gb|FL154236.1|FL154236
EST:     CAAGGCCCCAGAGACAGGCAGCCGGCGAGGCCCGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGGGGCAAGAAGGAACCCGAG
genomic: CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|211165539|gb|FL456882.1|FL456882
EST:     CGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGGGGCAAGAAGGAACCCGAG
genomic: CGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|78109695|gb|DV528111.1|DV528111
EST:     CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
genomic: CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|149080059|gb|EE169077.2|EE169077
EST:     CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
genomic: CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|110487038|gb|EE012240.1|EE012240
EST:     GCGAAGCAATG                         GATTTCAAGGGGGTCTCGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGA
genomic: GCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCT-GGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGA
EST: gi|76280583|gb|DV020151.1|DV020151
EST:     CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
genomic: CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|211305004|gb|FL154239.1|FL154239
EST:     CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
genomic: CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|149106054|gb|EE291707.2|EE291707
EST:     CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
genomic: CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|211307018|gb|FL154240.1|FL154240
EST:     CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGTGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
genomic: CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|71297616|gb|DR784759.1|DR784759
EST:     CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
genomic: CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|211305000|gb|FL154235.1|FL154235
EST:     CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
genomic: CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|148963213|gb|EE014191.2|EE014191
EST:     CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
genomic: CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|78121929|gb|DV540313.1|DV540313
EST:     CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
genomic: CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|78106806|gb|DV525224.1|DV525224
EST:     CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
genomic: CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|76281419|gb|DV020987.1|DV020987
EST:     CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
genomic: CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|67021064|gb|CO449813.1|CO449813
EST:     CAA-GTCCCAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGGGGCAAGAAGGAACCCGAG
genomic: CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|211307022|gb|FL154244.1|FL154244
EST:     CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
genomic: CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|149035101|gb|EE155087.2|EE155087
EST:     GGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
genomic: GGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|8367772|gb|BE050717.1|BE050717
EST:     GGCGAGGCGCGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
genomic: GGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|148963079|gb|EE014036.2|EE014036
EST:     CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
genomic: CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|30307202|gb|CD001875.1|CD001875
EST:     CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
genomic: CAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAG
EST: gi|211307019|gb|FL154241.1|FL154241
EST:     AAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAAGTG                         GATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGA
genomic: AAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAA-TGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGA

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: 108

GAGAGTGCGCTCGTCGACTCCACTCAGCTCTCTCGCTCACTCTCCTCCCCCAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAGCCGGAGCAGAACGGGCACGCCAACGGGGTCCAGAACCAGAAGAGGACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

GAGAGTGCGCTCGTCGACTCCACTCAGCTCTCTCGCTCACTCTCCTCCCCCAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAGCCGGAGCAGAACGGGCACGCCAACGGGGTCCAGAACCAGAAGAGGACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 144

GAGAGTGCGCTCGTCGACTCCACTCAGCTCTCTCGCTCACTCTCCTCCCCCAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAGCCGGAGCAGAACGGGCACGCCAACGGGGTCCAGAACCAGAAGAGGACCT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 91

GAGAGTGCGCTCGTCGACTCCACTCAGCTCTCTCGCTCACTCTCCTCCCCCAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgca ... gttctcccagGATTTCAAGGGGTTCTGGGAGTCCAGATTCGGTGGCAAGAAGGAACCCGAGCCGGAGCAGAACGGGCACGCCAACGGGGTCCAGAACCAGAAGAGGACCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAGTGCGCTCGTCGACTCCACTCAGCTCTCTCGCTCACTCTCCTCCCCCAAGGTCCTAGAGACAGGCAGCCGGCGAGGCGCGCCGCCGCGAAGCAATGgcaagttgcacgggtttcctattccccgccgccgcggcctctcgctcccctctctctgcgcggcctgctgactcccgtctccgcgttcgttctcccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA