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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATTTGAGAGGTTATTTCAATTCAACCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAGgtgagctaactttattatactccctccgtcaaatggatgataatgaatgtaaacatatacaaaacacatacatcaagtattgtatgaatccaccaattct...

Basic information

species Zea mays
transcript GRMZM2G099056_T01
intron # 22
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|6827336|gb|AW330979.1|AW330979
EST:     GGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAG                         ATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTACTGAAA
genomic: GGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAGgtgagctaac ... aatttttcagATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTACTGAAA
EST: gi|86469278|gb|DY235648.1|DY235648
EST:     AATTCAACCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAG                         ATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTACTGAAA
genomic: AATTCAACCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAGgtgagctaac ... aatttttcagATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTACTGAAA
EST: gi|50324254|gb|CO519380.1|CO519380
EST:     AATTCAACCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAG                         ATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTACTGAAA
genomic: AATTCAACCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAGgtgagctaac ... aatttttcagATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTACTGAAA
EST: gi|32846783|gb|CD986464.1|CD986464
EST:     AATTCAACCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAG                         ATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTAC
genomic: AATTCAACCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAGgtgagctaac ... aatttttcagATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTAC
EST: gi|50324253|gb|CO519379.1|CO519379
EST:     AATTCAACCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAG                         ATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTACTGAAA
genomic: AATTCAACCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAGgtgagctaac ... aatttttcagATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTACTGAAA
EST: gi|5608489|gb|AI902156.1|AI902156
EST:     AATTCAACCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAG                         ATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTACTGAAA
genomic: AATTCAACCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAGgtgagctaac ... aatttttcagATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTACTGAAA
EST: gi|5597302|gb|AI891400.1|AI891400
EST:     AATTCACCCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAG                         ATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTACTGAAA
genomic: AATTCAACCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAGgtgagctaac ... aatttttcagATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTACTGAAA
EST: gi|30032170|gb|CB834021.1|CB834021
EST:     AATTCACCCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAG                         ATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTACTGAAA
genomic: AATTCAACCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAGgtgagctaac ... aatttttcagATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTACTGAAA
EST: gi|31405680|gb|CD484412.1|CD484412
EST:     AATTCAACCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAG                         ATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTACTGAAA
genomic: AATTCAACCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAGgtgagctaac ... aatttttcagATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTACTGAAA
EST: gi|32933807|gb|CF038619.1|CF038619
EST:     AATTCAACCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAG                         ATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGT
genomic: AATTCAACCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAGgtgagctaac ... aatttttcagATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGT
EST: gi|30087811|gb|CB886017.1|CB886017
EST:     AATTCAACCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAG                         ATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTACTGAAA
genomic: AATTCAACCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAGgtgagctaac ... aatttttcagATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTACTGAAA

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: 229

CAATTTGAGAGGTTATTTCAATTCAACCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAGgtgagctaac ... aatttttcagATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTACTGAAATCCAGCTTATCTGGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 170

CAATTTGAGAGGTTATTTCAATTCAACCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAGgtgagctaac ... aatttttcagATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTACTGAAATCCAGCTTATCTGGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 154

CAATTTGAGAGGTTATTTCAATTCAACCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAGgtgagctaac ... aatttttcagATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTACTGAAATCCAGCTTATCTGGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 124

CAATTTGAGAGGTTATTTCAATTCAACCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAGgtgagctaac ... aatttttcagATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTACTGAAATCCAGCTTATCTGGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATTTGAGAGGTTATTTCAATTCAACCGGAAAGTTGACGAATTGACTTACACTATTGCTGCTGAGGAGgtgagctaactttattatactccctccgtcaaatggatgataatgaatgtaaacatatacaaaacacatacatcaagtattgtatgaatccaccaattct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaaaaca