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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtctccctctttgatcgtctatatggatggagtatgtgtgttgtgagttgagattgatcgaagcctgtctctgacgacgccgatgccgatgctcggtcgttgcgtgcagGACGTCGGCCGCTATGGCGGGATCAAGGTGTACGCCGTGCTCAGGGAAGACGGGGCCGAGTTCGCCCGGAACAACAACCTGGAGGCCCTGTTCCAGGTGG

Basic information

species Zea mays
transcript GRMZM2G171390_T04
intron # 1
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|71773513|gb|DR971413.1|DR971413
EST:     TGGCGCCGCGCCTACTCATTAAGCCCTCCCTCGCCTGCTTCTCCAGAAAG                         GACGTCGCCCGCTATGGCGGGATCAAGGTGTACGCCGTGCTCAGGGAAGAC
genomic: TGGCGCCGCGCCTGCTCATTAAGCCCTCCCTCGCCTGCTTCTCCAGAAAGgtgggtctcc ... ttgcgtgcagGACGTCGGCCGCTATGGCGGGATCAAGGTGTACGCCGTGCTCAGGGAAGAC
EST: gi|71447084|gb|DR828134.1|DR828134
EST:     TGGCGCCGCGCCTGCTCATTAAGCCCTCCCTCGCCTGCTTCTCCAGAAAG                         GACGTCGGCCGCTATGGCGGGATCAAGGTGTACGCCGTGCTCAGGGAAGAC
genomic: TGGCGCCGCGCCTGCTCATTAAGCCCTCCCTCGCCTGCTTCTCCAGAAAGgtgggtctcc ... ttgcgtgcagGACGTCGGCCGCTATGGCGGGATCAAGGTGTACGCCGTGCTCAGGGAAGAC
EST: gi|71764822|gb|DR962759.1|DR962759
EST:     CCCTCCCTCGCCTGCTTCTCCAGAAAG                         GACGTCGGCCGCTATGGCGGGATCAAGGTGTACGCCGTGCTCAGGGAAGAC
genomic: CCCTCCCTCGCCTGCTTCTCCAGAAAGgtgggtctcc ... ttgcgtgcagGACGTCGGCCGCTATGGCGGGATCAAGGTGTACGCCGTGCTCAGGGAAGAC
EST: gi|211346611|gb|FL190888.1|FL190888
EST:     TGGCGCCGCGCCTGCTCATTAAGCCCTCCCTCGCCTGCTTCTCCAGAAAG                         GACGTCGGCCGCTATGGCGGGATCAAGGTGTACGCCGTGCTCAGGGAAGAC
genomic: TGGCGCCGCGCCTGCTCATTAAGCCCTCCCTCGCCTGCTTCTCCAGAAAGgtgggtctcc ... ttgcgtgcagGACGTCGGCCGCTATGGCGGGATCAAGGTGTACGCCGTGCTCAGGGAAGAC
EST: gi|76935489|gb|DV174344.1|DV174344
EST:     TGGCGCCGCGCCTGCTCATTAAGCCCTCCCTCGCCTGCTTCTCCAGAAAG                         GACGTCGGCCGCTATGGCGGGATCAAGGTGTACGCCGTGCTCAGGGAAGAC
genomic: TGGCGCCGCGCCTGCTCATTAAGCCCTCCCTCGCCTGCTTCTCCAGAAAGgtgggtctcc ... ttgcgtgcagGACGTCGGCCGCTATGGCGGGATCAAGGTGTACGCCGTGCTCAGGGAAGAC
EST: gi|101394335|gb|EB819102.1|EB819102
EST:     TGGCGCCGCGCCTGCTCATTAAGCCCTCCCTCGCCTGCTTCTCCAGAAAG                         GACGTCGGCCGCTATGGCGGGATCAAGGTGTACGCCGTGCTCAGGGAAGAC
genomic: TGGCGCCGCGCCTGCTCATTAAGCCCTCCCTCGCCTGCTTCTCCAGAAAGgtgggtctcc ... ttgcgtgcagGACGTCGGCCGCTATGGCGGGATCAAGGTGTACGCCGTGCTCAGGGAAGAC
EST: gi|78085618|gb|DV514011.1|DV514011
EST:     TGGCGCCGCGCCTGCTCATTAAGCCCTCCCTCGCCTGCTTCTCCAGAAAG                         GACGTCGGCCGCTATGGCGGGATCAAGGTGTACGCCGTGCTCAGGGAAGAC
genomic: TGGCGCCGCGCCTGCTCATTAAGCCCTCCCTCGCCTGCTTCTCCAGAAAGgtgggtctcc ... ttgcgtgcagGACGTCGGCCGCTATGGCGGGATCAAGGTGTACGCCGTGCTCAGGGAAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatcgaagcctgtctctgacgacgccgatgccgatgctcggtcgttgcgtgcagGACGTCGGCCGCTATGGCGGGATCAAGGTGTACGCCGTGCTCAGGGAAGACGGGGCCGAGTTCGCCCGGAACAACAACCTGGAGGCCCTGTTCCAGGTGG
              ctctgac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtctccctctttgatcgtctatatggatggagtatgtgtgttgtgagttgagattgatcgaagcctgtctctgacgacgccgatgccgatgctcggtcgttgcgtgcagGACGTCGGCCGCTATGGCGGGATCAAGGTGTACGCCGTGCTCAGGGAAGACGGGGCCGAGTTCGCCCGGAACAACAACCTGGAGGCCCTGTTCCAGGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG