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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgactgctaagccttgcgctctaagttctttcctatgctcgtgtttcaaacgtcatctcgatgatatttgagtaatatgaactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGTGGCGGGATGGACGAGGACTAGTTTGACTGTGATTGTTCTCTTTGTGTAT

Basic information

species Zea mays
transcript GRMZM2G083095_T02
intron # 12
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|148978583|gb|EE026232.2|EE026232
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|148987523|gb|EE031385.2|EE031385
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGGGGGTTGACCAG                         ATCATTATGGGGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGG
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|33092559|gb|CF052553.1|CF052553
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|211519526|gb|FL441902.1|FL441902
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|113703848|gb|EE681352.1|EE681352
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|60357186|gb|DN224159.1|DN224159
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|60396537|gb|DN229406.1|DN229406
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGC
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGC
EST: gi|60358886|gb|DN225859.1|DN225859
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|7135329|gb|AW498031.1|AW498031
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCCCCGTGCTGCGGGTTGCCCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|7137645|gb|AW499199.1|AW499199
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|6539092|gb|AW225231.1|AW225231
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|211337113|gb|FK966354.1|FK966354
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAMG--G-CAAGGAGGTCCAAGAAGAGATGCCCAGCCTGG
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCA-GGAGGTCCAAGAAGAGATGCCCAGCCTGG
EST: gi|211337111|gb|FK966352.1|FK966352
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAMG--GTCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|33094754|gb|CF054748.1|CF054748
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|13177835|gb|BG349018.1|BG349018
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|4314488|gb|AI461542.1|AI461542
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|13178118|gb|BG349376.1|BG349376
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|71431586|gb|DR812636.1|DR812636
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|5688514|gb|AI941529.1|AI941529
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|148972050|gb|EE022890.2|EE022890
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGCCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|211337115|gb|FK966356.1|FK966356
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|78024594|gb|DV492981.1|DV492981
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|91053532|gb|EB163950.1|EB163950
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|211525262|gb|FL432917.1|FL432917
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|110194417|gb|EC876315.1|EC876315
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|211337114|gb|FK966355.1|FK966355
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|5919524|gb|AW054621.1|AW054621
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|60337628|gb|DN204601.1|DN204601
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|5006194|gb|AI712256.1|AI712256
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|149105114|gb|EE290597.2|EE290597
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCCCCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|10450915|gb|BE924839.1|BE924839
EST:     CCTATAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCTA-AAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|21759912|gb|BQ635453.1|BQ635453
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
EST: gi|4885786|gb|AI676906.1|AI676906
EST:     CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAG                         ATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT
genomic: CCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGT

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), 46 (downstream exon)
Score: 128

GTTCTTTGCCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGTGGCGGGATGGACGAGGACTAGTTTGACTGTGATTGTTCTCTTTGTGTAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 72

GTTCTTTGCCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGTGGCGGGATGGACGAGGACTAGTTTGACTGTGATTGTTCTCTTTGTGTAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 87

GTTCTTTGCCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGTGGCGGGATGGACGAGGACTAGTTTGACTGTGATTGTTCTCTTTGTGTAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 47

GTTCTTTGCCCTAAAATATTCTGCCGATGCCGCATGCACCGTGCTGCGGGTTGACCAGgtatgactgc ... aactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGTGGCGGGATGGACGAGGACTAGTTTGACTGTGATTGTTCTCTTTGTGTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgctcgtgtttcaaacgtcatctcgatgatatttgagtaatatgaactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGTGGCGGGATGGACGAGGACTAGTTTGACTGTGATTGTTCTCTTTGTGTAT
                             atatttgagtaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgactgctaagccttgcgctctaagttctttcctatgctcgtgtttcaaacgtcatctcgatgatatttgagtaatatgaactgtccagATCATTATGGCGAAGCCGGCAGGAGGTCCAAGAAGAGATGCCCAGCCTGGTGGCGGGATGGACGAGGACTAGTTTGACTGTGATTGTTCTCTTTGTGTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA