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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGACGCAAGGCTAGGGTTTCGCGCGACGCCGACGTCGACGGCAGCGAGGATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacccccgaaaccctacctgatatcacgatcgaagtgcgtggcggaaggttgtgtgcagggctggggttgtgtgcggcgctcgaatcgtgtgca...

Basic information

species Zea mays
transcript GRMZM2G129987_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|78111290|gb|DV529687.1|DV529687
EST:     ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAG                         ATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
genomic: ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacc ... tcatttgaagATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
EST: gi|31628006|gb|CD526397.1|CD526397
EST:     ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAG                         ATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
genomic: ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacc ... tcatttgaagATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
EST: gi|31664549|gb|CD573482.1|CD573482
EST:     ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAG                         ATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
genomic: ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacc ... tcatttgaagATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
EST: gi|19436724|gb|BM953134.1|BM953134
EST:     ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAG                         ATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
genomic: ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacc ... tcatttgaagATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
EST: gi|149009177|gb|EE041301.2|EE041301
EST:     ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAG                         ATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
genomic: ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacc ... tcatttgaagATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
EST: gi|91053239|gb|EB163657.1|EB163657
EST:     ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAG                         ATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
genomic: ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacc ... tcatttgaagATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
EST: gi|76011893|gb|DT939063.1|DT939063
EST:     ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAG                         ATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
genomic: ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacc ... tcatttgaagATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
EST: gi|71771230|gb|DR969167.1|DR969167
EST:     ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAG                         ATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
genomic: ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacc ... tcatttgaagATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
EST: gi|78082398|gb|DV510810.1|DV510810
EST:     ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAG                         ATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
genomic: ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacc ... tcatttgaagATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
EST: gi|211448244|gb|FK956529.1|FK956529
EST:     ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAG                         ATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
genomic: ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacc ... tcatttgaagATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
EST: gi|19057616|gb|BM736283.1|BM736283
EST:     ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAG                         ATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
genomic: ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacc ... tcatttgaagATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
EST: gi|19436292|gb|BM952702.1|BM952702
EST:     TGAGATGGCCGCTCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAG                         ATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
genomic: TGAGATGGCCGC-CGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacc ... tcatttgaagATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
EST: gi|71320398|gb|DR796949.1|DR796949
EST:     ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAG                         ATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
genomic: ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacc ... tcatttgaagATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
EST: gi|211448242|gb|FK956527.1|FK956527
EST:     ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAG                         ATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
genomic: ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacc ... tcatttgaagATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
EST: gi|211450351|gb|FK956532.1|FK956532
EST:     ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAG                         ATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
genomic: ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacc ... tcatttgaagATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
EST: gi|19436725|gb|BM953135.1|BM953135
EST:     ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAG                         ATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
genomic: ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacc ... tcatttgaagATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
EST: gi|91054843|gb|EB165261.1|EB165261
EST:     ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAG                         ATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
genomic: ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacc ... tcatttgaagATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
EST: gi|211448245|gb|FK956530.1|FK956530
EST:     ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAG                         ATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
genomic: ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacc ... tcatttgaagATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
EST: gi|76924244|gb|DV169873.1|DV169873
EST:     AGGAGCCTCTACGAG                         ATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
genomic: AGGAGCCTCTACGAGgtaaggcacc ... tcatttgaagATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
EST: gi|71315532|gb|DR794370.1|DR794370
EST:     ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAG                         ATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT
genomic: ATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacc ... tcatttgaagATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATAT

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: 322

GGGACGCAAGGCTAGGGTTTCGCGCGACGCCGACGTCGACGGCAGCGAGGATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacc ... tcatttgaagATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

GGGACGCAAGGCTAGGGTTTCGCGCGACGCCGACGTCGACGGCAGCGAGGATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacc ... tcatttgaagATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

GGGACGCAAGGCTAGGGTTTCGCGCGACGCCGACGTCGACGGCAGCGAGGATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacc ... tcatttgaagATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

GGGACGCAAGGCTAGGGTTTCGCGCGACGCCGACGTCGACGGCAGCGAGGATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacc ... tcatttgaagATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGACGCAAGGCTAGGGTTTCGCGCGACGCCGACGTCGACGGCAGCGAGGATGAGATGGCCGCCGCTCCTGCCGCCGCTGCGGGCAGGAGCCTCTACGAGgtaaggcacccccgaaaccctacctgatatcacgatcgaagtgcgtggcggaaggttgtgtgcagggctggggttgtgtgcggcgctcgaatcgtgtgca

- - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - accctacc