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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaaaacaaacgcaagccccaacaacctatctgcttttggttaaactggcttgtgcatggttcaataattcttatcaactttttctctatattattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCGACCGTCCAAACCATCCTAGAATATGATTGGTGGACTGCGATTAAATTGC

Basic information

species Zea mays
transcript GRMZM2G101250_T01
intron # 19
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|60399530|gb|DN232341.1|DN232341
EST:     ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAG                         TATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
genomic: ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAGgtgctttctc ... attattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
EST: gi|60358881|gb|DN225854.1|DN225854
EST:     ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAG                         TATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
genomic: ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAGgtgctttctc ... attattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
EST: gi|148934268|gb|EC878291.2|EC878291
EST:     ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAG                         TATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
genomic: ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAGgtgctttctc ... attattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
EST: gi|78121627|gb|DV540011.1|DV540011
EST:     ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAG                         TATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
genomic: ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAGgtgctttctc ... attattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
EST: gi|16916971|gb|BM073068.1|BM073068
EST:     ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAG                         TATTTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
genomic: ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAGgtgctttctc ... attattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
EST: gi|40302924|gb|CK347311.1|CK347311
EST:     ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAG                         TATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
genomic: ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAGgtgctttctc ... attattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
EST: gi|60358880|gb|DN225853.1|DN225853
EST:     ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAG                         TATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
genomic: ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAGgtgctttctc ... attattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
EST: gi|211220507|gb|FL445398.1|FL445398
EST:     ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAG                         TATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
genomic: ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAGgtgctttctc ... attattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
EST: gi|9254742|gb|BE345210.1|BE345210
EST:     ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAG                         TATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
genomic: ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAGgtgctttctc ... attattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
EST: gi|211312443|gb|FL348211.1|FL348211
EST:     AATGTGCTACTACAACGTATAACAG                         TATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
genomic: AATGTGCTACTACAACGTATAACAGgtgctttctc ... attattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
EST: gi|9254603|gb|BE345056.1|BE345056
EST:     ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAG                         TATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
genomic: ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAGgtgctttctc ... attattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
EST: gi|211181693|gb|FL465348.1|FL465348
EST:     ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAG                         TATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
genomic: ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAGgtgctttctc ... attattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
EST: gi|32834623|gb|CD974301.1|CD974301
EST:     ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAG                         TATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
genomic: ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAGgtgctttctc ... attattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
EST: gi|60353136|gb|DN220109.1|DN220109
EST:     ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAG                         TATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
genomic: ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAGgtgctttctc ... attattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
EST: gi|32930313|gb|CF035125.1|CF035125
EST:     ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAG                         TATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
genomic: ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAGgtgctttctc ... attattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
EST: gi|32833197|gb|CD972875.1|CD972875
EST:     ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAG                         TATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
genomic: ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAGgtgctttctc ... attattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
EST: gi|166554660|gb|EG170288.1|EG170288
EST:     ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAG                         TATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTG
genomic: ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAGgtgctttctc ... attattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTG
EST: gi|78121626|gb|DV540010.1|DV540010
EST:     ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAG                         TATCT-ATTTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTC
genomic: ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAGgtgctttctc ... attattacagTATCTTATTT-CCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTC
EST: gi|91056340|gb|EB166758.1|EB166758
EST:     ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAG                         TATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG
genomic: ATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAGgtgctttctc ... attattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCG

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), 47 (downstream exon)
Score: 43

AGATTGGATTAAAAATGGTGTCCACATCGGGAGTGGCAGAAAATATAAGGATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAGgtgctttctc ... attattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCGACCGTCCAAACCATCCTAGAATATGATTGGTGGACTGCGATTAAATTGC


Block sizes: 49 (upstream exon), 35 (downstream exon)
Score: 7

AGATTGGATTAAAAATGGTGTCCACATCGGGAGTGGCAGAAAATATAAGGATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAGgtgctttctc ... attattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCGACCGTCCAAACCATCCTAGAATATGATTGGTGGACTGCGATTAAATTGC


Block sizes: 40 (upstream exon), 44 (downstream exon)
Score: 18

AGATTGGATTAAAAATGGTGTCCACATCGGGAGTGGCAGAAAATATAAGGATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAGgtgctttctc ... attattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCGACCGTCCAAACCATCCTAGAATATGATTGGTGGACTGCGATTAAATTGC


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

AGATTGGATTAAAAATGGTGTCCACATCGGGAGTGGCAGAAAATATAAGGATTCCTATTTTCTTCAGGCGCAAGTAATGTGCTACTACAACGTATAACAGgtgctttctc ... attattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCGACCGTCCAAACCATCCTAGAATATGATTGGTGGACTGCGATTAAATTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggcttgtgcatggttcaataattcttatcaactttttctctatattattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCGACCGTCCAAACCATCCTAGAATATGATTGGTGGACTGCGATTAAATTGC
                                 ctttttctctatatt  CT-rich tract
                  aataattcttatcaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaaaacaaacgcaagccccaacaacctatctgcttttggttaaactggcttgtgcatggttcaataattcttatcaactttttctctatattattacagTATCTTATTTCCGAGCTACACACGAAGACTTGCACTTATACAGGTTGTTCGACCGTCCAAACCATCCTAGAATATGATTGGTGGACTGCGATTAAATTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- -aaacaaa
- - - - - -gcaagcc
- - - - - - - - - -caacaac
- - - - - - - - - - - - - - - ctgcttt
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatgg