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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGATCGCCATTTAGCTCTAGCATCTGAATTTGGTACAGCAAATGGAAAGGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgttttactgccactaggaatttgctattcatgttattccctgttttgttacttatctgcgtgtaatgattcttctgcag

Basic information

species Zea mays
transcript GRMZM2G063151_T01
intron # 3
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|211462608|gb|FK992343.1|FK992343
EST:     GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAG                         CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
genomic: GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
EST: gi|211457563|gb|FK992319.1|FK992319
EST:     GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAG                         CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
genomic: GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
EST: gi|211462609|gb|FK992344.1|FK992344
EST:     GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAG                         CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
genomic: GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
EST: gi|211462605|gb|FK992340.1|FK992340
EST:     GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAG                         CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
genomic: GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
EST: gi|13558490|gb|BG549846.1|BG549846
EST:     GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAG                         CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
genomic: GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
EST: gi|211465137|gb|FK992354.1|FK992354
EST:     GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAG                         CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
genomic: GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
EST: gi|211460083|gb|FK992329.1|FK992329
EST:     GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAG                         CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
genomic: GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
EST: gi|211460082|gb|FK992328.1|FK992328
EST:     GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAG                         CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
genomic: GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
EST: gi|211462610|gb|FK992345.1|FK992345
EST:     GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAG                         CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
genomic: GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
EST: gi|211457565|gb|FK992321.1|FK992321
EST:     GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAG                         CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
genomic: GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
EST: gi|211460080|gb|FK992326.1|FK992326
EST:     GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAG                         CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
genomic: GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
EST: gi|211457566|gb|FK992322.1|FK992322
EST:     GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAG                         CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
genomic: GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
EST: gi|211460085|gb|FK992331.1|FK992331
EST:     GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAG                         CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
genomic: GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
EST: gi|211462604|gb|FK992339.1|FK992339
EST:     GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAG                         CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
genomic: GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
EST: gi|211465138|gb|FK992355.1|FK992355
EST:     GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAG                         CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
genomic: GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
EST: gi|211462606|gb|FK992341.1|FK992341
EST:     GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAG                         CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
genomic: GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
EST: gi|211460077|gb|FK992323.1|FK992323
EST:     GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAG                         CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
genomic: GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
EST: gi|211460090|gb|FK992336.1|FK992336
EST:     GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAG                         CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
genomic: GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
EST: gi|211457564|gb|FK992320.1|FK992320
EST:     GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAG                         CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
genomic: GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
EST: gi|13249860|gb|BG360765.1|BG360765
EST:     GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAG                         CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
genomic: GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
EST: gi|211457560|gb|FK992316.1|FK992316
EST:     GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAG                         CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
genomic: GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
EST: gi|211462603|gb|FK992338.1|FK992338
EST:     GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAG                         CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
genomic: GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
EST: gi|211462614|gb|FK992349.1|FK992349
EST:     GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAG                         CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG
genomic: GGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATG

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: 45 (upstream exon), 49 (downstream exon)
Score: 22

TTTGATCGCCATTTAGCTCTAGCATCTGAATTTGGTACAGCAAATGGAAAGGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 101

TTTGATCGCCATTTAGCTCTAGCATCTGAATTTGGTACAGCAAATGGAAAGGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 119

TTTGATCGCCATTTAGCTCTAGCATCTGAATTTGGTACAGCAAATGGAAAGGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 92

TTTGATCGCCATTTAGCTCTAGCATCTGAATTTGGTACAGCAAATGGAAAGGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgtttta ... tcttctgcagCAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGATCGCCATTTAGCTCTAGCATCTGAATTTGGTACAGCAAATGGAAAGGGAAACACAAAGGTTGCCGGAAGAAACTCCAATGCTGTGTCTTTGGAAGgttcgttttactgccactaggaatttgctattcatgttattccctgttttgttacttatctgcgtgtaatgattcttctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG