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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatcttgaaggcactactatctgtttctgtgattgttaattttagtaggatatagtctgaccacattgtattgttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGGTAAGGAACATTTTATGACTTAACTCTTATTGATGCATGCTCAAATGCTCAC

Basic information

species Zea mays
transcript GRMZM2G050961_T04
intron # 3
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|74233447|gb|DT641361.1|DT641361
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGGTA
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGGTA
EST: gi|211485846|gb|FK973438.1|FK973438
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGA
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGA
EST: gi|74237817|gb|DT645731.1|DT645731
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGGTA
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGGTA
EST: gi|13558000|gb|BG549356.1|BG549356
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGGAGTTGAGGCTGGGAAGAAGGT
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGGT
EST: gi|166483222|gb|EG111081.1|EG111081
EST:     CCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATAGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGGT
genomic: CCAAAATCTGCTGTTAAGTTTGAGAGATATCTGAT-GGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGGT
EST: gi|166409968|gb|EG192262.1|EG192262
EST:     CTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGGT
genomic: CTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgattgttaattttagtaggatatagtctgaccacattgtattgttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGGTAAGGAACATTTTATGACTTAACTCTTATTGATGCATGCTCAAATGCTCAC
                          gtctgac  putative branch site (score: 3)
     tgttaattttagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagatcttgaaggcactactatctgtttctgtgattgttaattttagtaggatatagtctgaccacattgtattgttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGGTAAGGAACATTTTATGACTTAACTCTTATTGATGCATGCTCAAATGCTCAC

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