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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgccctctcccggccggtctccccacttccgtccctccttctctcgcgccacgttactgaccgaccgaccccacttctcttccctttcccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACCAAGCCGTGCAGCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGT

Basic information

species Zea mays
transcript GRMZM2G010044_T02
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|71772889|gb|DR970812.1|DR970812
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGCAG                       
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGT-C--CAGgtccgccctc ... ccgccagc
EST: gi|148955521|gb|EC901145.2|EC901145
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGCAG                       
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGT-C--CAGgtccgccctc ... ccgccagc
EST: gi|211185238|gb|FL072192.1|FL072192
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCAC-A-----AG                         AAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
EST: gi|91051662|gb|EB162080.1|EB162080
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         AAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
EST: gi|211187633|gb|FL072202.1|FL072202
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         AAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
EST: gi|148958467|gb|EC904705.2|EC904705
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         C
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcag-
EST: gi|148958467|gb|EC904705.2|EC904705
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         C
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcag-
EST: gi|211190029|gb|FL072209.1|FL072209
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         AAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
EST: gi|76012112|gb|DT939282.1|DT939282
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         AAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
EST: gi|211185232|gb|FL072186.1|FL072186
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         AAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
EST: gi|211185240|gb|FL072194.1|FL072194
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         AAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
EST: gi|31355882|gb|CD440239.1|CD440239
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         AAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
EST: gi|211187626|gb|FL072195.1|FL072195
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         AAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
EST: gi|211187637|gb|FL072206.1|FL072206
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         AAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
EST: gi|211185236|gb|FL072190.1|FL072190
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         AAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
EST: gi|31354069|gb|CD438426.1|CD438426
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGCAG                       
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGT-C--CAGgtccgccctc ... ccgccagc
EST: gi|211187631|gb|FL072200.1|FL072200
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         AAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
EST: gi|211187638|gb|FL072207.1|FL072207
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         AAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
EST: gi|76909966|gb|DV163627.1|DV163627
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         AAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
EST: gi|211187634|gb|FL072203.1|FL072203
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         AAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
EST: gi|211187628|gb|FL072197.1|FL072197
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCAC-A-----AG                         AAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
EST: gi|211185235|gb|FL072189.1|FL072189
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         AAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
EST: gi|211187639|gb|FL072208.1|FL072208
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         AAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
EST: gi|211185239|gb|FL072193.1|FL072193
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         AAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACC

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: 37 (upstream exon), 48 (downstream exon)
Score: 7

TCGCAGGGTGTTCGACCCTTCGCCCGCGCGCCCTCACGACATGGCCTCCTCCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACCAAGCCGTGCAGCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGT


Block sizes: 43 (upstream exon), 45 (downstream exon)
Score: 13

TCGCAGGGTGTTCGACCCTTCGCCCGCGCGCCCTCACGACATGGCCTCCTCCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACCAAGCCGTGCAGCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGT


Block sizes: 42 (upstream exon), 25 (downstream exon)
Score: 2

TCGCAGGGTGTTCGACCCTTCGCCCGCGCGCCCTCACGACATGGCCTCCTCCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACCAAGCCGTGCAGCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGT


Block sizes: 35 (upstream exon), 48 (downstream exon)
Score: 4

TCGCAGGGTGTTCGACCCTTCGCCCGCGCGCCCTCACGACATGGCCTCCTCCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACCAAGCCGTGCAGCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgcgccacgttactgaccgaccgaccccacttctcttccctttcccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACCAAGCCGTGCAGCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGT
           tactgac  putative branch site (score: 4)
                     ccgaccccacttctct  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccgccctctcccggccggtctccccacttccgtccctccttctctcgcgccacgttactgaccgaccgaccccacttctcttccctttcccgccagcagAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACCAAGCCGTGCAGCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGCCGGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCGCCG